Investigations of the supercoil-selective DNA binding of wild type p53
suggest a novel mechanism for controlling p53 function
Miroslav Fojta1
, Hana Pivonkova1
, Marie Brazdova1,2
, Katerina Nemcova1
, Jan Palecek1,3
and
Borivoj Vojtesek4
1
Laboratory of Biophysical Chemistry and Molecular Oncology, Institute of Biophysics, Academy of Sciences of the Czech Republic,
Brno, Czech Republic; 2
Department of Tumor Virology, Heinrich-Pette-Institute for Experimental Virology and Immunology at the
University of Hamburg, Hamburg, Germany; 3
Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, UK;
4
Masaryk Memorial Cancer Institute, Brno, Czech Republic
The tumor suppressor protein, p53, selectively binds to
supercoiled (sc) DNA lacking the specific p53 consensus
binding sequence (p53CON). Using p53 deletion mutants,
we have previously shown that the p53 C-terminal DNAbinding
site (CTDBS) is critical for this binding. Here we
studied supercoil-selective binding of bacterially expressed
full-length p53 using modulation of activity of the p53
DNA-binding domains by oxidation of cysteine residues (to
preclude binding within the p53 core domain) and/or by
antibodies mapping to epitopes at the protein C-terminus (to
block binding within the CTDBS). In the absence of antibody,
reduced p53 preferentially bound scDNA lacking
p53CON in the presence of 3 kb linear plasmid DNAs or
20 mer oligonucleotides, both containing and lacking the
p53CON. Blocking the CTDBS with antibody caused
reduced p53 to bind equally to sc and linear or relaxed
circular DNA lacking p53CON, but with a high preference
forthep53CON.Thesameimmunecomplexofoxidizedp53
failed to bind DNA, while oxidized p53 in the absence of
antibody restored selective scDNA binding. Antibodies
mapping outside the CTDBS did not prevent p53 supercoilselective
(SCS) binding. These data indicate that the CTDBS
is primarily responsible for p53 SCS binding. In the absence
of the SCS binding, p53 binds sc or linear (relaxed) DNA via
the p53 core domain and exhibits strong sequence-specific
binding. Our results support a hypothesis that alterations to
DNA topology may be a component of the complex cellular
regulatory mechanisms that control the switch between
latent and active p53 following cellular stress.
Keywords: monoclonal antibodies; p53 latency; redox state;
supercoil-selective DNA binding; tumor suppressor protein
p53.
The tumor suppressor protein p53 has been called Ôthe
guardian of the genomeÕ due to its functions in maintaining
genetic integrity of cells (reviewed in [1–4]). Mutations of the
p53 gene are frequently connected with malignant transformation.
Under stress conditions, wild type p53 acts as
transcriptional activator for genes including p21, gadd45,
bax and mdm2 [5]. In addition, it has been proposed that in
normal cells p53 participates in DNA replication, recombination
and repair in a transcription-independent manner
[6,7].
The biological activities of p53 are closely connected
with its ability to interact with DNA. The protein is
organized into several functional domains [8]. The
N-terminal domain contains a transactivation region
[amino acids (aa) 1–42] and a proline-rich region (aa
61–94), and mediates interactions with other transcription
factors or the mdm2 protein. The evolutionary conserved
core domain (CD; aa  100–300) is involved in sequencespecific
binding to p53 response elements (consensus
sequences; p53CONs) that occur within promoters of p53
downstream genes [9]. This domain also exhibits sequence
nonspecific binding to internal regions of single-stranded
and double-stranded DNA [10], conformation-specific
interaction with DNA motifs mimicking early recombination
intermediates [11,12], hairpin DNA structures [13]
and insertion/deletion mismatches [14]. The C-terminal
part of the protein contains a tetramerization domain (aa
325–356) and the basic DNA-binding site (CTDBS; aa
363–382). The CTDBS binds DNA sequence nonspecifically
but exhibits a remarkable selectivity for certain
DNA structures, including single-stranded DNA ends
[10], single-stranded gaps within double-stranded DNA
molecules [15], c-irradiated [16] or cis-platinated DNA
[17,18], and supercoiled DNA [19–24].
Regulation of the p53 DNA-binding activities is
achieved through post-translational modifications of the
protein molecule [4,25–27]. In the unmodified protein, a
segment of the C-terminus (aa 369–383), overlapping with
Correspondence to M. Fojta, Institute of Biophysics, Academy of
Sciences of the Czech Republic, Kra´ lovopolska´ 135, CZ-612 65 Brno,
Czech Republic. Fax: +420 5 41211293, Tel.: +420 5 41517197,
E-mail: fojta@ibp.cz
Abbreviations: aa, amino acids; CD, core domain; CON, 20 mer ODN
spanning the p53CON; CTDBS, C-terminal DNA-binding site; fl, full
length; linDNA, linearized DNA; ocDNA, open circular DNA; ODN,
oligodeoxyribonucleotide; NODN, nonspecific 20 mer ODN; p53red
,
reduced p53; p53ox
, oxidized p53; p53CON, p53 consensus DNA
binding sequence; relDNA, relaxed DNA; scDNA, supercoiled DNA;
SCS, supercoil-selective.
(Received 2 June 2004, revised 27 July 2004, accepted 4 August 2004)
Eur. J. Biochem. 271, 3865–3876 (2004) Ó FEBS 2004 doi:10.1111/j.1432-1033.2004.04323.x
the p53 CTDBS [28], acts as a negative regulator of
sequence-specific binding and is connected with the
apparent p53 ÔlatencyÕ typically observed in unstressed
cells. Latency of p53 has been explained either by
allosteric control of the CD via intramolecular protein–
protein interactions [25,29] or by strong nonspecific p53–
DNA binding mediated by the unmodified CTDBS,
preventing the p53 core from interacting efficiently with
the consensus sequences [30–32]. The negative regulatory
effect of the C-terminus is abolished by phosphorylation
[25,33], acetylation [34,35], deletion [25] or blocking by
noncovalent effectors including antibodies [26,36,37],
cellular proteins such as Ref1 [26], or short nucleic acid
molecules [10,28,30]. Another mechanism that may be
involved in regulating DNA binding activity of the CD is
connected with changes of the protein redox state
[9,21,26,38,39]. The p53 core contains 10 cysteine residues;
these residues are absent in other parts of the p53
molecule [40]. In general, the reduced state of cysteines is
critical for the proper DNA binding function of the p53
core. It has been shown that extensive oxidation of the
p53 thiol groups results in a loss of DNA binding within
the p53 core while controlled oxidation of Cys277 leads
to altered sequence-specificity of the p53–DNA interaction
[9]. DNA binding activities within the p53
C-terminus are not prevented by protein oxidation
[21,22,39].
Full length (fl) p53 and the protein deletion variants
possessing the CTDBS exhibit a distinct interaction with
supercoiled (sc) DNA (independent of the presence of the
p53CON), forming stable p53–DNA complexes that can be
observed as band ladders in agarose gels [19–21,23].
Electron microscopy revealed formation of nucleoprotein
filaments at higher protein/DNA ratios [23]. In competition
experiments with linear (lin) DNA, fl p53 binds scDNA with
a high preference (supercoil-selective; SCS binding) [20,23].
Recent observations suggest that DNA topology and DNA
conformation transitions related to DNA supercoiling also
markedly affect p53 binding to the p53CONs, resulting in
either stimulation [41] or inhibition [42] of sequence-specific
interactions. By means of protein deletion studies [23], the
ability of p53 to recognize scDNA was attributed primarily
to the protein C-terminus. Truncated p53 forms lacking the
CTDBS were unable to selectively bind scDNA, while
isolated p53 C-terminal domains exhibited SCS binding. It
has been proposed that SCS binding involves cooperative
interactions of the oligomeric p53 C-terminal domain with
two segments of the DNA double helix within the plectonemic
DNA superhelix, and stabilization of the complexes
(filaments) by further protein–DNA and protein–protein
interactions [23].
In this paper we employed redox modulation of the
p53 CD and antibody manipulations at the protein
C-terminus to study binding of bacterially expressed full
length p53 protein to various topological forms of DNA
either containing or lacking the p53CON. We demonstrate
that the p53 CTDBS is critical for p53 SCS binding while
the p53 CD is responsible for the supercoil nonselective
DNA binding of p53 immune complexes in which the
CTDBS is blocked by an antibody. Possible roles of p53
SCS DNA binding in the regulation of its biological
activities are discussed.
Materials and methods
DNA samples
Supercoiled (sc) DNA of plasmid pBSK(–) (not containing
p53CON) was isolated form Escherichia coli DH5a cells and
purified by CsCl/ethidium bromide gradient ultracentrifugation.
Superhelix density of the scDNA estimated from
chloroquine agarose gels [43] was about )0.06. Linear
DNAs were prepared by SmaI (Takara) cleavage of the
pBSK(–) or pPGM1 (containing a p53CON identical to the
CON oligonucleotide below) plasmids. Relaxed covalently
closed circular (rel) DNA was prepared using wheat germ
topoisomerase I (Promega). To generate open circular (oc)
DNA, the scDNA sample was irradiated with c-rays from a
Chisostat 60
Co source (Chirana1 , Brno, Czech Republic) in
10 mM Tris/EDTA buffer; the dose (about 40 Gy) was
adjusted empirically to achieve 50% relaxation of the
scDNA. Synthetic 20 mer oligonucleotides (ODNs), the
specific 5¢-AGACATGCCTAGACATGCCT-3¢ (CON)
and nonspecific 5¢-GCATCATAGCGCATCATAGC-3¢
(NODN), including their complementary strands, were
purchased from VBC Genomics2 (Vienna, Austria).
Monoclonal antibodies
The following anti-p53 mouse monoclonal antibodies
(mAbs) were generated against full length p53 protein
expressed in bacteria (DO-1, Bp53-10.1, Bp53-6.1, Bp53-
30.1) and against synthetic peptide (ICA9). The method of
development of antibodies was described in [44]. DO-1
binds to an epitope (aa 21–25) in the N-terminal region of
the protein (Fig. 1) [44,45]. The other mAbs bind to the
C-terminal region of p53, including ICA9 (aa 388–393) [46],
PAb421 (aa 371–380) [45,47], Bp53-10.1 and Bp53-30.1
(aa 375–379), and Bp53-6.1 (aa 381–390) (Fig. 1) [48,49].
Fig. 1. Scheme of the domain structure of a subunit of full length p53
protein. The two p53 DNA binding sites, the core domain (CD; aa
80–310) and the basic C-terminal DNA binding site (CTDBS; aa 363–
382), are indicated by grey boxes. The cross-hatched region (aa 325–
356) is the p53 tetramerization domain. Diagonally hatched boxes
indicate epitopes of mAbs DO-1 (aa 21–25), Bp53-10.1 (aa 375–379),
Bp53-6.1 (aa 381–390) and ICA-9 (aa 388–393). The p53 CD contains
cysteine residues (indicated by ÔSHÕ) which are the objects for redox
modulation of the protein. The C-terminal region is expanded for
better resolution of the CTDBS and the mAb epitopes.
3866 M. Fojta et al. (Eur. J. Biochem. 271) Ó FEBS 2004
The mAbs were purified from cell culture supernatants or
ascites by means of affinity chromatography using either
protein G-Sepharose (Pharmacia) or protein L-Sepharose
(Pierce).
Purification of p53
Human full length p53 protein (wild type) was expressed
in bacterial E. coli BL21/DE3 cells containing plasmid
pT77Hup53. The cells were grown at 20 °C using a two-step
induction with isopropyl thio-b-D-galactoside to limit protein
aggregation. The protein was purified according to a
modified protocol reported by Hupp et al. [36]. Protein was
eluted from a Heparin-Sepharose Hi-Trap column (Pharmacia)
by a 40 mL linear gradient of KCl at 0.5 M, followed
by gel filtration through Superdex HR 10/10 (Pharmacia).
Purity of the p53 preparation was checked by SDS/PAGE.
The protein concentration was determined densitometrically
from Coomassie Blue R-250 stained gels, using bovine
serum albumin as a standard.
Modification of the p53 protein
Oxidation of cysteine residues was achieved through
incubation of the protein with 1 mM diamide (Sigma) in
50 mM KCl, 5 mM Tris, 0.5 mM EDTA, 0.01% (v/v) Triton
X-100 (pH 7.6) at 0 °C for 20 min. Reduced p53 was
prepared by incubation with 2 mM dithiothreitol under the
same conditions. Immune complexes of reduced or oxidized
p53 were prepared by addition of the relevant mAb to the
reaction mixture, followed by a 20 min incubation (more
details in Results and Figure legends).
DNA binding assay
scDNA (400 ng) of pBSK(–) plasmid were mixed with the
pretreated p53 samples (see above) at p53 tetramer/DNA
molar ratios between 2.5 and 10, and incubated for 30 min
on ice to reach equilibrium. In competition experiments
400 ngof theplasmidcompetitor DNAs or 50 ng of 32
P endlabeledODNs,wereaddedtothesamplesat
thesametimeas
the scDNA. After binding, the samples were loaded on 1 or
1.3% agarose gel containing 0.33· Tris/Borate/EDTA buffer,
pH 8.0. Agarose gel electrophoresis was performed for 3
or 10 h at 120 V and 4 °C. (The higher agarose concentration
and longer separation times were used in the sc/linear
(lin) competition assays to achieve better separation of the
nucleoprotein complexes. It should be noted that under the
given conditions, linDNA migrates faster than scDNA of
the same length.) Gels were stained with ethidium bromide
and photographed. Radioactively labeled competitor ODNs
were detected by autoradiography of the gel.
Immunoblotting analysis of p53–DNA complexes
Agarose gels were blotted onto nitrocellulose membrane
BioTrace NT (Pall Life Sciences, Ann Arbor, MI, USA)3 in
3 M NaCl, 0.3 M sodium citrate (pH 7.0) on a vacuum
blotting system (Bio-Rad) under 80 mPa. The membrane
was then blocked with 5% low-fat powdered milk4 in NaCl/
Pi solution and p53 was detected with primary rabbit
polyclonal antibody CM1 (diluted 1 : 5000), followed by a
horseradish peroxidase conjugated anti-rabbit IgG (Sigma)
diluted 1 : 5000. Bands were visualized with the ECL
detection system (Amersham). Band intensities were quantified
by IMAGE-QUANT software.
Results
Effects of monoclonal antibodies on binding of reduced
and oxidized p53 to scDNA
Full length p53 was preincubated with either 2 mM dithiothreitol
(p53red
) or 1 mM diamide (p53ox
) followed by
addition of a 5-fold molar excess (relative to the p53
tetramer) of one of the following antibodies: DO-1 (mapping
to aa 21–25), ICA-9 (aa 388–393), Bp53-6.1 (aa 381–
390) or Bp53-10.1 (aa 375–379) (Fig. 1). Then, scDNA of
plasmid pBSK(–) (lacking the p53CON) was added (ratio
of p53/scDNA ¼ 5) and the effects of the antibodies on
formation of p53–scDNA complexes were followed using
mobility shift assay in agarose gel. Reduced p53 alone
(Fig. 2A, lane 2) as well as all of its immune complexes
(lanes 3–6) bound to scDNA, yielding band ladders in the
ethidium stained gel (Fig. 2A). Based on the electrophoretic
mobility shift and immunoblotting data and on parallel
electron microscopic observations, we have concluded
previously that individual retarded bands in the ladders
differ in number of the p53 tetramers bound per scDNA
molecule [20,21,23,50]. In the presence of the mAbs, the
retarded bands were supershifted providing evidence for the
formation of ternary mAb–p53red
–scDNA complexes [37].
The antibodies alone (in absence of the p53 protein) had no
effect on the mobility of scDNA (Fig. 2B, lanes 11 and 12,
for Bp53-10.1 and ICA-9, respectively).
Oxidized p53 alone (Fig. 2A, lane 7) as well as its immune
complex with the p53 N-terminus mapping mAb DO-1
(lane 8) bound to scDNA, showing similar binding when
compared to p53red
(lane 2) and p53red
–DO-1 (lane 3),
respectively. Strikingly, effects of the mAbs mapping to the
protein C-terminus on formation of p53ox
–scDNA complexes
differed markedly, depending on the positions of
their epitopes relative to the CTDBS (Fig. 1). ICA-9
(Fig. 2A, lane 9), mapping to the extreme C-terminus of
p53, caused about 40% inhibition of p53ox
–scDNA binding
(data obtained from densitometric tracing of the free
scDNA band). The complex of p53ox
with Bp53-6.1
(mapping to epitope aa 381–390 just next to the CTDBS,
Fig. 1) exhibited only 20–25% of scDNA binding (Fig. 2A,
lane 10), compared to p53ox
in the absence of mAb. The
stronger inhibition caused by Bp53-6.1 was in qualitative
agreement with previous observations made with the
p53(320–393) fragment [23]. With both ICA-9 and Bp53-
6.1, highly visible, distinct bands exhibiting characteristic
supershifts could be identified (Fig. 2A, lanes 9 and 10). On
the contrary, the mAb Bp53-10.1 (within the CTDBS) fully
inhibited binding of p53ox
to scDNA under the same
conditions (Fig. 2A, lane 11). Strong inhibition of the
p53ox
–scDNA binding was also exhibited by the mAbs
PAb421 and Bp53-30.1 (not shown), whose epitopes
overlap with that of Bp53-10.1 [37,49].
Effects of the antibody concentration on binding of
p53ox
to scDNA were examined for the mAbs Bp53-10.1
and ICA-9 (Fig. 2B,C). Increasing the Bp53-10.1/p53 ratio
Ó FEBS 2004 Redox and antibody modulation of p53–scDNA binding (Eur. J. Biochem. 271) 3867
(Fig. 2B, lanes 3–6) resulted in gradual decrease of the
p53ox
–scDNA binding. Although supershifting of the band
of p53–scDNA complex was observed at the Bp53-10.1/
p53 tetramer ratio ‡1.25, further additions of the antibody
resulted in diminishing of the band intensity (Fig. 2B, lanes
4–6). Intensity of the band of free scDNA simultaneously
increased, at Bp53-10.1/p53 ¼ 2.5 (lane 6) reaching 93% of
the intensity of the scDNA band in the absence of p53 (lane
1). On the contrary, ICA-9 did not inhibit binding of the
p53ox
to scDNA in the same antibody concentration range
(Fig. 2B, lanes 7–10). Instead, continuous retardation of
the p53–scDNA complexes was observed with increasing
the ICA-9/p53 ratio up to 5. Intensity of the scDNA band
only slightly increased with the ICA-9 concentration
(Fig. 2B,C). The results suggest that amino acid residues
375–379 (the Bp53-10.1 epitope) within the p53 CTDBS
are of critical importance for binding of the oxidized p53 to
scDNA. Blocking of this segment with Bp53-10.1 resulted
in a strong inhibition of the p53ox
–scDNA complex
formation. On the other hand, antibody binding outside the
CTDBS did not prevent formation of the p53ox
–scDNA
complexes.
Influence of mAbs on the supercoil-selective DNA
binding of reduced p53
Although p53red
was capable of binding to scDNA in the
presence of either of the mAbs tested, the results shown in
Fig. 2 did not reveal whether this binding was supercoilselective.
We therefore performed competition experiments
involving sc and linear pBSK(–) DNA (sc/lin competition
assay) to evaluate the influence of individual mAbs on the
preference of p53red
for scDNA. Figure 3 shows that at the
p53/scDNA ratio ¼ 2, p53red
alone bound scDNA selectively,
yielding a detectable complex only with scDNA
(Fig. 3A, lane 3). This SCS binding was also retained in the
presence of antibodies DO-1, Bp53-6.1 and ICA-9 (Fig. 3A,
lanes 4, 6 and 7), i.e. the mAbs mapping to epitopes outside
the CTDBS. In all cases, supershifted complexes were
observed with scDNA but not with linDNA. On the
contrary, immune complexes of p53red
and Bp53-10.1
bound both sc and linDNA, yielding retarded bands of
about the same intensities (Fig. 3A, lane 5). The behavior of
antibody-free p53red
and of p53red
–Bp53-10.1 immune
complexes was also compared in competition experiments
with circular relaxed DNAs (at p53/scDNA ¼ 5). The
pBSK(–) DNA was either treated with topoisomerase I
[generating relaxed covalently closed circular DNA (relDNA);
Fig. 3B], or irradiated by c-rays inducing single
strand breaks [resulting in formation of open circular DNA
(ocDNA); Fig. 3C]. Similarly to the sc/lin competition assay
(Fig. 3A), the mAb-free p53red
bound scDNA with a high
preference, producing no detectable bands of the relDNA–
p53 or ocDNA–p53 complexes. On the other hand, p53red
–
Bp53-10.1 bound both relDNA and ocDNA in the presence
of scDNA (Fig. 3B,C). Analogous results were observed
with the mAbs PAb421 and Bp53-30.1 that also bind within
the CTDBS (not shown). Therefore, blocking the p53
CTDBS by mAbs resulted in loss of the protein preference
for the scDNA, although these p53red
immune complexes
were still capable of binding to both scDNA and the relaxed
DNA forms (Figs 2 and 3).
Fig. 2. Influence of monoclonal antibodies on binding of reduced and
oxidized p53 to scDNA.77 (A) Effects of monoclonal antibodies recognizing
different epitopes in p53 on binding of reduced or oxidized p53
to pBSK(–) scDNA. Protein was preincubated with 2 mM dithiothreitol
(p53red
) or 1 mM diamide (p53ox
) in 10 lL of 50 mM KCl,
5 mM Tris/HCl, 0.5 mM EDTA, 0.01% (v/v) Triton X-100 (pH 7.8) on
ice for 20 min. Then, the mAbs were added (200 ng per sample) and
the mixtures were incubated on ice for 20 min, followed by subsequent
addition of 400 ng of scDNA (molar ratio p53 tetramer/DNA ¼ 5)
and incubation of the samples on ice for 30 min. After electrophoretic
separation in 1% agarose, DNA was stained with ethidium bromide
and the gel was photographed. Lanes 2–6, reduced p53; lanes 7–11,
oxidized p53; lane 1, scDNA only; lanes 2 and 7, no mAb; lanes 3 and
8, DO-1; lanes 4 and 9, ICA-9; lanes 5 and 10, Bp53-6.1; lanes 6 and 11,
Bp53-10.1. Bands denoted as ÔscÕ and ÔocÕ correspond to free monomeric
scDNA and open circular DNA, respectively. Species migrating
between sc and ocDNA are p53–scDNA or mAb–p53–scDNA complexes.
(B,C) Effects of increasing amounts of the mAbs Bp53-10.1 and
ICA-9 on binding of oxidized p53 to scDNA. (B) Ethidium stained
agarose gel: lane 1, scDNA only; lane 2, no mAb; lanes 3–6, Bp53-10.1;
lanes 7–10, ICA-9. mAb/p53 tetramer molar ratios: lanes 3 and 7, 0.5;
lanes 4 and 8, 1.25; lanes 5 and 9, 2.5; lanes 6 and 10, 5. Control
samples loaded on lanes 11 and 12 contained scDNA and 200 ngÆmL)1
of Bp53-10.1 or ICA-9, respectively, but no p53. (C) Graph showing
the effects of Bp53-10.1 or ICA-9 concentration on relative bound
fraction of scDNA [data calculated from densitometric tracing of the
free scDNA bands in (B)]. For other details, see Fig. 2A.
3868 M. Fojta et al. (Eur. J. Biochem. 271) Ó FEBS 2004
To examine the effects of Bp53-10.1 or ICA-9 on the
p53red
preference for scDNA at different antibody concentrations,
the sc/lin competition experiments were performed
at a ratio of p53/scDNA ¼ 5 (Fig. 4A,B). Under these
conditions, p53red
alone again bound scDNA with a high
preference, apparently producing no linDNA complex
(Fig. 4A,B, lane 3). At Bp53-10.1/p53 ¼ 0.5, a faint band
of the p53–linDNA complex appeared on the blot (lane 4).
Starting from a Bp53-10.1/p53 ratio of 1.25 (lane 5), the
protein preference for scDNA was lost. Immune complexes
of p53 with ICA-9 exhibited a different behavior (Fig. 4A,B,
lanes 8–11). A weak band of p53–linDNA appeared on the
blot at ICA-9/p53 ¼ 1.25 (lane 9) and the intensity of this
band steadily increased with the ICA-9 concentration; the
p53 preference for scDNA simultaneously decreased slightly
(Fig. 4). Nevertheless, at the highest ICA-9/p53 ratio (¼ 5,
lane 11) p53 still exhibited distinctly preferential scDNA
binding, providing 10–15-times higher intensity of the p53–
scDNA bands as compared to p53–linDNA (Fig. 4C; data
obtained from densitometric tracing of the blot on Fig. 4B).
Taken together, these results revealed an essential role of the
CTDBS for p53 SCS binding and moreover indicated that
blocking of only a part of the Bp53-10.1 epitopes within the
p53 tetramer (at the mAb/p53 tetramer molar ratio of 1.25)
was sufficient for a loss of the p53red
preference for scDNA.
Effects of p53 oxidation on SCS binding
We further examined the effect of p53 oxidation on its
preference for scDNA (in the absence of mAbs, at p53/
scDNA ratios of 3 and 6, Fig. 5). Oxidized p53 exhibited
similar binding to scDNA and linDNA in the absence of
the other DNA form (Fig. 5, lanes 8–11). Nevertheless, in
the sc/lin competition assay, p53ox
bound scDNA with a
strong preference, yielding a faint band of p53ox
–linDNA
complex only at p53/DNA ¼ 6 (Fig. 5B, lane 13).
Distinctly supercoil-selective DNA binding was thus
retained by p53ox
, although the overall p53 DNA
interactions were partially decreased due to oxidation of
the protein cysteine residues.
Fig. 3. Influence of monoclonal antibodies on the supercoil-selective DNA binding of reduced p53.88 (A) Effects of different mAbs on preferential
binding of reduced p53 to scDNA in competition with linDNA. Both forms of the pBSK(–) DNA (400 ng of each) were added to the protein and
subsequently preincubated with dithiothreitol and/or with the given antibody at the same time. After photographing of the ethidium stained DNA
(as in Fig. 2), the gel was blotted onto nitrocellulose membrane. Visualization of the p53 with anti-p53 rabbit polyclonal antibody CM1 and
secondary anti-rabbit IgG peroxidase conjugate using the ECL technique. Left, ethidium stained gel; right panel, immunoblot: lane 1, scDNA only;
lane 2, linDNA only; lanes 3–7, sc/lin competition for p53 in the presence of: lane 3, no mAb; lane 4, DO-1; lane 5, Bp53-10.1; lane 6, Bp53-6.1; lane
7, ICA-9. The samples were run on 1.3% agarose gel and the p53/scDNA ratio was 2 : 1. For other details see Fig. 2. (B,C) Analogous competition
assays performed with topoisomerase relaxed (rel) or open circular (oc) pBSK(–) DNA instead of the lin DNA. (B) Lane 1, scDNA only; lane 2,
relDNA only lanes 3–4, sc/rel competition for p53: lane 3, no antibody; lane 4, Bp53-10.1. (C) Lane 1, 1 : 1 mixture of sc and ocDNA, no p53; lanes
2 and 3, sc/oc competition for p53: lane 2, no antibody; lane 3, Bp53-10.1. The smear below the p53–Bp53-10.1–scDNA complexes on the
immunoblots corresponds to the DNA–unbound p53 immune complex. The samples were run on 1% gel with p53/scDNA ¼ 5; other details as in
(A). Arrows indicate positions of p53–mAb complexes with the competitor DNAs.
Ó FEBS 2004 Redox and antibody modulation of p53–scDNA binding (Eur. J. Biochem. 271) 3869
Competition between supercoiled DNA and p53CON
for p53
We performed further competition assays to compare
binding affinities of p53red
(in the absence of antibodies)
and of its Bp53-10.1 immune complex to pBSK(–) scDNA
(not containing the p53CON) with the sequence-specific
binding of the two p53 forms. We used competitor DNAs
containing the p53CON either within a linear  3 kb
plasmid pPGM1 (Fig. 6A,B), or in a 20 mer doublestranded
oligonucleotide (Fig. 6C,D).
The lin pPGM1 DNA was used in a molar ratio of 1 : 1
to the sc pBSK(–) DNA. In the absence of mAb, p53red
bound pBSK(–) scDNA with a remarkable preference
(Fig. 6A,B, lanes 3–5). On the other hand, p53red
–Bp53-10.1
complex exhibited a strong bias towards the lin pPGM1
DNA (Fig. 6A,B, lanes 6–8) under the same conditions,
indicating that this p53 immune complex bound to the
p53CON within the linDNA with a higher affinity than to
the scDNA lacking the consensus sequence. Competition
experiments involving the 20 mer p53CON oligonucleotide
(CON) provided qualitatively the same results. The presence
of a 20-fold molar excess of the 32
P-labeled ODNs
(regardless of their sequences) was apparently without effect
on p53red
–scDNA binding (Fig. 6C, lanes 3 and 5).
Autoradiogram of the agarose gel revealed the formation
of p53–ODN complexes only in the absence of scDNA
(Fig. 6D, lanes 4 and 6). A strikingly different behavior was
exhibited by p53–Bp53-10.1. In the presence of the CON,
binding of the p53 immune complex to scDNA was fully
abolished (Fig. 6C, lane 8). Supershifted spots corresponding
to the CON–p53–Bp53-10.1 complexes appeared on the
autoradiogram both in the presence and absence of scDNA
(Fig. 6D, lanes 8 and 9). On the other hand, NODN did not
inhibit formation of the scDNA–p53–Bp53-10.1 complexes
(Fig. 6C, lane 10), and spots corresponding to the NODN–
p53–Bp53-10.1 complexes were detected only in the absence
of scDNA (Fig. 6D, lane 11). It should be emphasized that
no radioactive signal matched the ethidium-stained band
ladders corresponding to the p53–scDNA complexes
(Fig. 6D, lanes 3, 5, 7 and 10).
Results shown in Fig. 6 suggest that p53red
with an
unmodified C-terminus (i.e. in the absence of Bp53-10.1)
bound more strongly to scDNA not containing p53CON
than to the specific sequence in both long plasmid
linDNA molecule and the 20 mer ODN. On the other
hand, the immune complex p53–Bp53-10.1 bound preferentially
to the p53CON. This agrees well with inactivation
of the p53 CTDBS (responsible for the p53 SCS
binding) and activation of the protein sequence-specific
Fig. 4. Effects of the concentration of the mAbs Bp53-10.1 and ICA-9 on preferential binding of reduced p53 to scDNA in competition with linDNA.
(A) Ethidium stained agarose gel. (B) Immunoblot: lane 1, scDNA only; lane 2, linDNA only; line 3, no mAb; lanes 4–7, Bp53-10.1; lanes 8–11,
ICA-9; mAb/p53 tetramer ratios: lanes 4 and 8, 0.5; lanes 5 and 9, 1.25; lanes 6 and 10, 2.5; lanes 7 and 11, 5. (C) Graph showing the effects of mAbs
concentration on p53 preference for scDNA [expressed as ratios of the intensities of bands of p53–scDNA/p53–linDNA complexes on the blot (B)].
For other details, see Fig. 2.
3870 M. Fojta et al. (Eur. J. Biochem. 271) Ó FEBS 2004
DNA binding by Bp53-10.1 [37]. Experiments with the
CON oligonucleotide did not provide any sign of
formation of tentative ternary CON–p53–scDNA complexes,
in which p53 CD would bind the oligonucleotide
while CTDBS bound scDNA.
Discussion
Redox and antibody modulation of DNA binding
of p53 core and C-terminal domains
In our recent papers [20,23], we used p53 deletion mutants
to identify the roles of p53 domains in supercoil-selective
DNA binding. It was shown that the isolated C-terminal
domain of p53 (amino acids 320–393) binds scDNA with a
high preference, while p53 lacking the CTDBS did not,
suggesting that it is the p53 CTDBS which is crucial for
strong SCS binding. The protein deletion studies are useful
for characterization of the isolated p53 DNA binding sites
but cannot directly confirm their roles in SCS DNA binding
of full length p53 that represents a more complex entity. We
have therefore combined the deletion experiments with a
parallel study of contributions of the p53 CD and the
CTDBS to the SCS binding of fl p53. The DNA binding
activities of the two domains in fl p53 were separately
modulated by a thiol-oxidizing agent diamide and by
monoclonal antibodies mapping to epitopes within the
protein C-terminus. It has been established previously that
the redox state of p53 is essential for its sequence-specific
DNA binding [21,26,38–40]. Oxidation of cysteine residues
in the p53 CD results in substantial changes in the protein
structure, including release of zinc ion from the CD
[21,22,38,50,51] and adopting a mutant-like conformation
unable to bind the p53CON [38]. The p53 structural changes
due to thiol oxidation are reversible under certain conditions
[9,21,26] and redox modulation has been taken into
consideration as one of the possible mechanisms involved
in the complexities of p53 control in vivo [9,21,26,40]. Our
preliminary results (M. Fojta, M. Brazdova & H. Pivonkova,
unpublished data) showed that sequence-nonspecific
binding of the isolated p53 CD [p53(94–312)] or C-terminally
truncated p53(1–363) to both linDNA and scDNA
lacking the p53CON are also strongly inhibited by p53
oxidation. Because the C-terminal domain does not contain
cysteine residues, fl p53ox
retained the ability to bind DNA
via this site [21,22,38,39]. On the other hand, the CTDBS
can be Ôswitched offÕ by antibodies mapping to epitopes
within it (such as antibodies PAb421 and Bp53-10.1
[37,49,52,53]).
The p53 CTDBS is critical for preferential binding
of full length p53 to scDNA
Our oxidation and antibody-interference experiments
suggest that fl p53ox
can bind scDNA unless a segment
of its CTDBS is blocked by mAbs Bp53-10.1 (Fig. 2),
PAb421 or Bp53-30.1. In the presence of these mAbs,
binding of fl p53ox
to scDNA or linDNA (regardless of
the presence or absence of the p53CON) was abolished,
suggesting a crucial role of the CTDBS in p53ox
DNA
binding. Immune complexes of p53red
with mAbs mapping
to the protein C-terminus bound scDNA in the
absence of linDNA efficiently, regardless of the epitope
position (Fig. 2). However, the sc/lin competition assay
(Figs 3 and 4) revealed striking differences in DNA
binding of p53red
–Bp53-10.1 and p53red
complexes with
Fig. 5. Effect of the p53 redox state on preferential
binding to scDNA. (A) Ethidium
stained agarose gel. (B) Immunoblot: lane 1,
scDNA only; lane 14, linDNA only; lanes 2–7,
reduced p53; lanes 8–13, oxidized p53; lanes
2–3 and 8–9, p53 binding to linDNA alone;
lanes 4–5 and 10–11, p53 binding to scDNA
alone; lanes 6–7 and 12–13, competition between
sc and linDNA; lanes 2, 4, 6, 8, 10
and 12, p53/DNA ¼ 3 : 1; lanes 3, 5, 7, 9, 11
and 13, p53/DNA ¼ 6 : 1. For other details,
see Fig. 2.
Ó FEBS 2004 Redox and antibody modulation of p53–scDNA binding (Eur. J. Biochem. 271) 3871
mAbs binding outside the CTDBS. The former p53red
immune complex bound both sc and linDNA, both
lacking the p53CON, and also oc or relDNA (Fig. 3B,C),
without significant preference for DNA form. Titration
experiments showed that blocking of only two of the
CTDBS copies in the p53 tetramer (by one molecule of
the divalent antibody) was sufficient for a strong decrease
of SCS binding (Fig. 4). This was in qualitative accordance
with our previous suggestions that efficient p53 SCS
binding requires cooperative protein–DNA interactions in
the multivalent form of the protein CTDBS, conferred by
the oligomeric state of the deletion protein constructs
[23]. It should nevertheless be noted that the tetrameric fl
p53 with two copies of CTDBS blocked by the mAb
behaved differently than dimeric constructs of p53
C-terminal domain used previously [23]. The latter were
able to bind scDNA with a high preference in the sc/lin
competition assay. A comparison of results shown in this
paper in Figs 2B and 4 suggests that the presumably
semisaturated Bp53-10.1 immune complex of p53ox
could
bind scDNA, yielding a supershifted band of the
nucleoprotein complex (Fig. 2B, lane 4); on the other
hand, binding of p53red
at the same p53/mAb ratio was
not supercoil-selective (Fig. 4, lane 5). It can be speculated
that in the semisaturated immune complex of fl p53,
the remaining two CTDBS copies were not capable of
efficient cooperative binding to scDNA for steric reasons.
Steric interference of bulky antibody molecules bound to
the protein C-terminus can also be the source of a partial
inhibition of scDNA binding in the p53–ICA-9 immune
complex (Figs 2B,C and 4).
We reported previously [21,22] that oxidized insect cellexpressed
p53 was able to bind scDNA in the absence of
linDNA, albeit with a partially decreased affinity. In this
Fig. 6. Competition between scDNA (lacking
p53CON) and p53CON for reduced p53 or its
Bp53–10.1 immune complex. (A,B) Binding of
p53 to sc pBSK(–) in the presence of linear
pPGM1 DNA (containing the p53CON): lane
1, scDNA alone; lane 2, lin pPGM1 alone;
lanes 3–8, both DNAs (molar ratio 1 : 1);
lanes 3–5, no antibody; lanes 6–8, Bp53-10.1;
lanes 3 and 6, p53/scDNA ¼ 2.5; lanes 4 and
7, p53/scDNA ¼ 5; lanes 5 and 8, p53/
scDNA ¼ 10. (A) Ethidium stained gel. (B)
Immunoblot. (C,D) Binding of p53 to sc
pBSK(–) in the presence of p53CON in
20 mer oligonucleotides: lane 1, scDNA alone;
lanes 2–6, no antibody; lanes 7–11, Bp53-10.1;
lanes 1, 2 and 7, no ODN; lanes 3, 4, 8 and 9,
CON; lanes 5, 6, 10 and 11, nonspecific ODN
(NODN). The ODNs were radioactively endlabeled
and applied in about eightfold molar
excess (20 ng per sample), as compared to
scDNA. In the autoradiogram (D), horizontal
bars represent superimposition of the ethidium
stained bands in (C); p53/scDNA ¼ 5.
For other details, see Fig. 2.
3872 M. Fojta et al. (Eur. J. Biochem. 271) Ó FEBS 2004
paper we demonstrate that the same behavior is exhibited by
post-translationally unmodified bacterially expressed p53.
Moreover, we show for the first time that p53ox
retains its
preferential binding to scDNA in the sc/lin competition
assay (Fig. 5). Therefore, Ôswitching offÕ the DNA binding
activity of the p53 CD by thiol oxidation does not result in
abolishment of the p53 SCS DNA binding, as long as the
protein CTDBS is available (Fig. 7B). Conversely, blocking
the CTDBS of p53red
by mAbs causes loss of SCS binding
(Fig. 7C). Taken together, these observations demonstrate
that the tetrameric p53 CTDBS is critical for SCS binding
of full length p53.
Supercoil-nonselective DNA binding of the full length
p53 complex with Bp53-10.1 is located within the protein
core domain
The behavior of the reduced form of the immune complex
p53–Bp53-10.1 was analogous to that earlier established for
p53 deletion constructs lacking the CTDBS but possessing
the CD, such as p53(94–312) [20], p53(1–363) or p53(45–
349) [23]. These constructs bound scDNA with apparently
no or only weak preference in competition experiments
with lin or relaxed circular DNAs (in the absence of the
p53CON) [20,23]. Competition experiments involving the
p53CON (Fig. 6) support the idea that the p53 CD is
primarily responsible for the supercoil-nonselective DNA
binding of p53–Bp53-10.1). Both the linear plasmid pPGM1
DNA and the CON oligonucleotide were strong inhibitors
of binding of this p53 immune complex to pBSK(–) scDNA,
but not of p53–scDNA binding in the absence of mAb,
indicating that the sequence-specific DNA-binding site was
essential for the interaction of p53–Bp53-10.1) with scDNA
lacking the p53CON. When this site was occupied by the
CON ODN, the p53 immune complex completely lost its
ability to bind to scDNA. Similar results were obtained with
the p53(1–363) deletion mutant (not shown).
It has been established that post-translational modifications
(phosphorylation [4,27,29] or acetylation [4,34]) of the
negative-regulating region within the p53 C-terminal
domain, overlapping with the CTDBS [28], result in
activation of the sequence-specific binding activity of the
CD [4,26,29,31,32,37]. Blocking of this site by antibodies
such as PAb421 [29] or Bp53-10.1 [37,49], or its deletion
[30,36], have a similar effect. The differences between the
post-translationally unmodified fl p53 and its Bp53-10.1
immune complex (or the C-terminally truncated p53
constructs [23]) can thus also be discussed in terms of p53
activation. In the presence of the activating mAb Bp53-10.1
[37], the affinity for p53CON increased and the immune
complex (possessing only the CD available for DNA
binding) bound preferentially to the pPGM1 linDNA
(Fig. 6A,B) or to the CON ODN (Fig. 6C,D) in the
presence of pBSK(–) scDNA. Activated p53 might also
exhibit increased binding to degenerative p53CON-like
sequences that are present in the pBSK(–) plasmid (including
three p53CON half-sites containing a single base
mismatch [17]). Such ÔsemispecificÕ p53–DNA interactions
may partially contribute to the nonpreferential p53–Bp53-
10.1 binding to both sc and lin pBSK(–) DNA (Figs 3
and 4).
Is the core domain involved in the SCS DNA binding
of unmodified full length p53?
Results presented in this paper together with those published
previously [20–23] lead us to conclude that the p53
CTDBS is primarily responsible for the p53 SCS DNA
binding. On the other hand, the ability of the p53 CD to
recognize some DNA conformational motifs, including
those characteristic for negatively scDNA, was discussed
([20,23] and refs therein). The isolated p53 CD (aa 94–312)
exhibited a certain degree of preference for scDNA in the sc/
lin competition assay [20]. The p53 CD may therefore take
part in the SCS DNA binding of fl p53.
One of the earlier proposed models of p53 latency, the
ÔstericÕ hypothesis [30], was based on mutual exclusivity of
the p53 CD and CTDBS in DNA binding, implying that
strong interactions of the unmodified CTDBS with nonspecific
DNA prevent the CD from binding p53CON.
However, there are growing amounts of data inconsistent
with such a concept. Recent observations suggest that one
p53 tetramer can interact with one DNA molecule by both
DNA binding sites at the same time. In a double-stranded
ODN possessing single-stranded overhangs, a p53 tetramer
bound the overhangs via its C-terminal domains, simultaneously
interacting with the central part of the ODN via its
core domains [15]. Using fluorescence correlation spectroscopy
it has been shown that the CD of a C-terminally
unmodified p53 can interact with long double-stranded
DNA molecules sequence nonspecifically [31]. These data
recently resulted in the formulation of a Ôtwo-siteÕ model of
p53 latency [31,32], involving simultaneous interaction of
both core and C-terminal domains of ÔlatentÕ p53 with
nonspecific DNA sequences. In addition, other observations
suggest that the p53 C-terminus may stimulate sequencespecific
binding to some p53 response elements within
topologically constrained DNA molecules [41,54].
Structure-selective interactions of the CTDBS with DNA
Fig. 7. Schematic summarization of the effects of cysteine oxidation
within the p53 CD and mAb binding within the p53 CTDBS on the SCS
DNA binding of bacterially expressed fl p53. Arrows indicate available
DNA binding sites. (A) p53red
in the absence of mAbs exhibits a highly
selective scDNA binding; (B) p53ox
in the absence of the mAbs also
displays the SCS DNA binding; (C) p53red
preference for scDNA is
lost due to blocking of a part of the CTDBS by a mAb; (D) p53ox
does not efficiently bind DNA when its CTDBS is blocked by the
mAb.
Ó FEBS 2004 Redox and antibody modulation of p53–scDNA binding (Eur. J. Biochem. 271) 3873
facilitated p53 binding to a p53 response element within
small DNA circles [54] or to p53CONs adopting non-B
structures in ODNs [13,55,56] as well as within large
plasmid scDNA molecules [41]. The absence of ternary
complexes of CON–p53red
–scDNA demonstrated in this
paper (Fig. 6) suggests that upon p53red
binding to scDNA
via its CTDBS, the CD could not behave as an independent
DNA binding site. There is thus no analogy between
binding of the p53 C-terminus to the known noncovalent
p53 activators of sequence-specific DNA binding and the
interaction of p53 with scDNA. An explanation for this
observation may be that the p53 sequence-specific DNA
binding site was occupied, taking part in the fl p53red
interaction with the scDNA molecule.
Possible consequences of the p53 SCS DNA binding
in the regulation of p53 biological activities
It has been proposed [6,7] that p53 may play a dual role in
cells, acting either as a transcription factor under stress
conditions (in its ÔinducedÕ, ÔactivatedÕ state, being able to
bind DNA mainly sequence-specifically) or taking part
directly in control of DNA replication, recombination
[11,12] or repair (in a transcription-independent pathway) in
unstressed cells. The latter function has been attributed to
the ÔnoninducedÕ (ÔlatentÕ) forms of p53, exhibiting primarily
conformation-selective DNA binding [6,7,55,56]. Interactions
of some p53 mutants with non-B DNA structures
specific for certain elements of chromatin architecture may
be related to the p53 Ôgain of functionÕ effect [57,58]. The
possible involvement of p53 nucleoprotein filament formation
(that correlates with the p53 SCS binding) in DNA
recombination was discussed [23].
The relationships between DNA supercoiling and biological
functions are well established [59–62]. In the nuclei of
eukaryotic cells, rearrangements of chromatin structure
occur during fundamental processes such as DNA replication,
recombination, DNA repair or transcription and are
connected with dynamic changes in DNA supercoiling [60–
62]. Interactions of p53 with DNA will therefore be likely to
change in synchrony with local alterations in DNA
topology. In particular, our observations that post-translationally
unmodified p53 binds strongly to scDNA suggest
an additional mechanism for the induction of p53 as a
sequence-specific transcription factor. The recently proposed
Ôtwo-siteÕ [31,32] as well as the ÔstericÕ [30] models of
p53 latency involve strong interactions of p53 CTDBS with
genomic DNA molecules, which prevents the p53 core
domain from binding to p53 response elements. As the
affinity of post-translationally unmodified p53 (regardless of
its redox state) to scDNA is much higher than to relaxed
(lin) DNA molecules, it is likely that DNA supercoiling in
the nuclei contributes to p53 ÔlatencyÕ by sequestering p53 to
scDNA. Sequestering of p53 will be overcome by relaxation
of the local superhelical stress (due to chromatin rearrangement
processes or, for instance, as a result of exposure to
genotoxic agents that induce single- or double-strand DNA
breaks), allowing post-translational modifications and subsequent
activation of sequence-specific binding to p53
response elements. Strong binding of p53 to supercoiled
DNA domains in the nucleus might also result in escape of
p53 from the protein modification machinery to maintain
the latent state, in keeping with the observations that p53activation
in vivo is highly variable between different tissues
and cell populations within tissues [63,64]. This ÔsequestrationÕ
model for determining the balance between ÔlatentÕ and
active p53 is not incompatible with the two previously
proposed models, and each may act in combination or
separately in different cells under different conditions of
growth and/or stress to regulate the overall p53 response
pathway. Changes of DNA superhelicity and their impact
on p53–DNA interactions, including the p53 SCS binding
outside the p53 response elements [19–23,37,50] and DNA
topology-dependent conformation transitions of some p53inducible
promoters [41,42], together with post-translational
modifications of the p53 protein, might thus represent a
complex p53 regulatory network.
Acknowledgements
This work was supported by a grant of GACR 204/02/0734 and 301/02/
0831, IGA MH CR NC/7574-3 and NC7131-3, and by grants
S 5004009 and Z 5004920. The authors thank Prof. Emil Palecek and
Dr Phil Coates for their helpful advice and critical reading of the
manuscript.
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