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Volume 271, Number 26,
Issue of June 28, 1996
pp. 15443-15450
©1996 by The American Society for Biochemistry and Molecular Biology, Inc.
The Hepatitis B Virus Transactivator Protein, HBx, Interacts with
Single-stranded DNA (ssDNA)
BIOCHEMICAL CHARACTERIZATIONS OF THE HBx-ssDNA INTERACTIONS*
(Received for publication, August 8, 1995, and in revised form, March 13, 1996)
Ishtiaq
Qadri
,
Marilyn E.
Ferrari
§ and
Aleem
Siddiqui
¶
From the Departments of Microbiology, § Biochemistry,
Biophysics, and Genetics, the Program in Molecular Biology, University
of Colorado, Health Sciences Center, B 172, Denver, Colorado 80262
ABSTRACT
INTRODUCTION
EXPERIMENTAL PROCEDURES
RESULTS
DISCUSSION
FOOTNOTES
Acknowledgments
REFERENCES
ABSTRACT
Human hepatitis B virus X protein, HBx, is widely
acknowledged as a transcriptional transactivator. While HBx has been
shown to increase gene expression in trans, it is generally
believed that it does not bind double-stranded DNA. Using several
experimental approaches, we show that HBx interacts with
single-stranded DNA in a manner that is not sequence-specific. Various
heterologous single-stranded DNA (ssDNA) oligonucleotides were able to
compete in HBx-ssDNA interactions in gel shift assays.
Escherichia coli non-sequence-specific, single-stranded DNA
binding protein, E. coli SSB, displaced the HBx-ssDNA
interactions, confirming the ability of HBx to interact with
single-stranded DNA in a non-sequence-specific manner. We have further
characterized the HBx-ssDNA interactions under various biochemical
conditions. These include the effects of mono- and divalent cations,
the effect of cardiolipin and heparin, pH and temperature dependence,
and variations in the incubation time. HBx bound more tightly to
d(pyrimidines)25 than to d(purines)25, a
property that is characteristic of other single-stranded DNA-binding
proteins (SSBs). Collectively the results presented here provide the
first evidence of HBx's interaction with ssDNA. The biochemical
parameters of these interactions were similar to those of known viral
and cellular SSBs.
INTRODUCTION
Hepatitis B virus (HBV)1 infection is
associated with chronic hepatitis and development of hepatocellular
carcinoma (Beasley et al., 1981 ). Over 300 million
individuals are infected with HBV worldwide. HBV is the smallest known
human virus, with a 3.2-kilobase genome, and it encodes four major open
reading frames, pre-C/C, pre-S2/S, P, and X (reviewed by Nasal and
Schaller (1993) ). HBV DNA in the virion is partially double-stranded
and held in circular conformation. The native molecule has a fixed 5
end, whereas the 3 end of the plus (+) strand has variable termini in
each molecule. HBV replicates via a reverse transcription mechanism
using longer than genome-length, pregenomic RNA. The reverse
transcriptase/RNase H activities are encoded by P open reading frame. P
protein is covalently attached to the ( ) strand DNA via its terminal
protein (TP) domain (reviewed by Nasal and Schaller (1993) ).
One of the open reading frames of the HBV genome encodes a protein
termed HBx. It is now generally acknowledged that HBx provided in
trans can increase gene expression. The transactivation function
of HBx has been tested in the context of a wide variety of viral and
cellular promoter/enhancer elements (Twu and Schloemer (1987) , Zahm
et al. (1988) , Spandau and Lee (1988) , Siddiqui et
al. (1989) , Colgrove et al. (1989) , Hu et
al. (1990) , Rossner (1992) and references therein). One of the
possible mechanisms by which HBx may function was first shown to be via
protein-protein interactions with the transcriptional factors
ATF-2/CREB (Maguire et al., 1991 ). Subsequently,
interactions of HBx with several cellular proteins were reported. These
include p53 tumor suppressor protein (Wang et al., 1994 ),
RNA polymerase subunit RPB5 (Cheong et al., 1995 ), universal
transcriptional factor, TATA-binding protein (TBP) (Qadri et
al., 1995 ), and a putative DNA repair protein, UV-DDB (Lee
et al., 1995 ). Recently, we have shown that HBx interacts
with the DNA helicase components (ERCC2 and ERCC3) of basal
transcriptional factor TFIIH and stimulates the DNA helicase activity
of TFIIH.2 All of the proteins with which
HBx has been shown to form heteromeric complexes reside in the nucleus.
Although not shown by direct protein-protein interactions, the
activities of HBx have been shown to influence the events relevant to
signal transduction pathways (Cross et al., 1993 ; Kekule
et al., 1993 ; Natoli et al., 1994 ; Benn and
Schneider, 1994 ). However, the cellular targets of HBx in signal
transduction pathways have not been identified.
Transcription initiation and promoter clearance by RNA ploymerase
II requires the melting of the DNA template (Conaway and
Conaway, 1993 ). HBx interactions with the components of basal
transcription factors TBP and TFIIH suggest a possible role of HBx at
these stages of transcription. The formation and maintenance of
single-stranded DNA within the nucleus requires the action of
single-stranded DNA binding proteins (SSBs) (Yagil, 1991 ). The role of
SSBs would be to initiate and maintain localized single-stranded
conformations during important cellular functions such as DNA
replication, transcription, recombination, and DNA excision repair.
Here, we report that HBx interacts with ssDNA in a manner that is not
sequence-specific. This study further details characterization of
various biochemical parameters of HBx's interaction with ssDNA. These
include the effects of mono- and divalent cations, the effect of
cardiolipin and heparin, pH and temperature dependence, and variations
in the incubation time. Our results show that HBx-ssDNA interactions
are tighter at low concentrations of mono- and divalent salt and weaker
at higher salt concentrations, consistent with the predicted salt
dependence for protein-DNA interactions. The HBx-ssDNA interaction is
stable up to 45 °C. Heparin failed to compete completely with DNA
for HBx binding, suggesting that HBx interactions with DNA are
stabilized by significant interactions with the DNA bases. The
biological relevance of HBx interaction with ssDNA remains to be
investigated.
EXPERIMENTAL PROCEDURES
Plasmids
Construction of full-length HBx fusion with
glutathione S-transferase gene (pGST-X) has been described
previously (Qadri et al., 1995 ). In the plasmid pSPX, the
X-gene was cloned within the polylinker in pSP65 in front of the SP6
promoter for in vitro translation of HBx. HBV DNA was
extracted from HBV-positive human serum by phenol extraction and
ethanol precipitation procedure.
Oligonucleotides
A 26-nucleotide-long oligonucleotide
termed RXR-S containing the sequence 5 -AGTAAACAGTACATGAACCTTTACCC-3 ,
corresponding to nucleotides 1125-1150 of enhancer I of HBV genome was
used in the mobility shift assay. The competitor oligonucleotides are
as follows with the following sequence: AS, antisense
5 -GGGTAAAGGTTCATGTACTGTTTACT-3 ; FV-S,
5 -AGTAAACAGTAACATGAACCTTTACCC-3 ; FV-AS,
5 -GGGTAAAGGTTCATGTTACTGTTTACT-3 ; and X-P,
5 -AAGAGATGATTAGGCAGAGGT-3 . T7-P/P and SP6-P/P primers were
purchased from Promega. Competitor oligonucleotides described above and
oligonucleotides of d(A)25, d(C)25,
d(G)25, and d(T)25 were synthesized at the core
facility of the Department of Microbiology, University of Colorado
Health Sciences Center (Denver, CO).
Chemicals and Enzymes
SDS, acrylamide,
N,N -methylene-bisacrylamide, Coomassie Brilliant
Blue R-250, ammonium persulfate, and TEMED were purchased from Bio-Rad.
Hydrocholoric acid (HCl), potassium chloride (KCl), sodium chloride
(NaCl), magnesium chloride (MgCl2), and potassium hydroxide
(KOH) were from Fisher. Heparin, cardiolipin, HEPES,
phenylmethylsulfonyl fluoride (PMSF),
isopropyl-1-thio- -D-galactopyranoside, dithiothreitol
(DTT), glutathione, Nonidet P-40, Triton X-100, and ATP were purchased
from Sigma. Protein assay reagents and SDS-PAGE molecular weight
markers were purchased from Bio-Rad. [ -32P]ATP was
purchased from ICN. Avian myeloblastosis virus reverse transcriptase
and T4 polynucleotide kinase were purchased from Promega.
Chromatographic Supports
Glutathione
S-transferase affinity beads were purchased from Pharmacia
Biotech Inc. Single-stranded DNA agarose was purchased from Life
Technologies, Inc.
Electrophoretic Mobility Gel Shift Assay
Single-stranded
oligonucleotides were labeled with [ -32P]ATP in the
presence of T4 polynucleotide kinase. The radiolabeled probe was
gel-purified, and an aliquot of 1 × 103 cpm (0.1 ng; 0.484 nM) was used for a binding reaction with either GST or
GST-X fusion proteins. The 32P-labeled single-stranded DNA
probe and fusion proteins were incubated in a buffer in a 25-µl
reaction volume that contained, 100 mM KCl, 20 mM HEPES (pH 7.9), 5 mM MgCl2, 5%
glycerol (v/v), 2 mM DTT, and 0.2 mM PMSF at
30 °C for 30 min. The ssDNA-HBx complexes were resolved in a
nondenaturing 6% polyacrylamide gel in 0.5 × TBE running buffer at
4 °C. The gels were dried and exposed to x-ray film (XAR; Kodak) at
80 °C with an intensifying screen. Unless specified otherwise, the
GST-HBx concentration used in the gel mobility experiments was 4 × 10 8 M. The results were analyzed using a
PhosphorImager by direct exposer of the gel. To quantitate the DNA
represented by the different bands, a box surrounding each band was
defined, and the relative densities of the bands were calculated. The
fraction of protein-DNA complex (X) was calculated from the
ratio the intensity of the shifted band to the total DNA. The binding
affinity was estimated from the HBx concentration required to bind half
of the DNA (Carey, 1991 ).
UV Cross-linking of HBx with ssDNA
A 26-nucleotide-long
(RXR-S) ssDNA probe was labeled at the 5 termini with
[ -32P]ATP in the presence of T4 polynucleotide kinase.
The probe was incubated with either GST or GST-X proteins for 30 min at
30 °C and irradiated in a UV Stratalinker model 1800 (Stratagene) at
312 nm for 30 min at 4 °C. After incubation and UV-irradiation, the
covalently cross-linked proteins with radiolabeled ssDNA were separated
on 13% SDS-PAGE and autoradiographed.
Purification of GST Fusion Proteins
The GST fusion proteins
were purified as described previously (Smith and Johnson, 1988 ). To
dissociate contaminant Escherichia coli proteins, the
binding of bacterial lysates to glutathione S-transferase
affinity beads and subsequent washing was conducted in the presence of
1.2 M NaCl to remove nonspecific binding of bacterial
proteins to HBx. An additional step of purification was included, which
involved passing the purified GST-X fusion protein through a
single-stranded DNA agarose column. The protein fractions from ssDNA
agarose were first eluted in 700 mM KCl, 25 mM
HEPES (pH 7.9), 1 mM DTT, 1 mM EDTA, and 0.2 mM PMSF and then dialyzed in a buffer containing either no
monovalent cations or 100 mM KCl and 25 mM
HEPES, pH 7.9, 10% glycerol (v/v), 1 mM ATP, 1 mM DTT, and 0.2 mM PMSF.
RESULTS
HBx Interacts with Single-stranded Nucleic Acids
Using
several standard methodologies, we demonstrate the ability of HBx to
bind single-stranded nucleic acids. The HBx interaction with
single-stranded nucleic acids was first examined by electrophoretic
mobility shift assay (EMSA), using a glutathione
S-transferase-HBx fusion protein. The results of gel
mobility shift assays described in Fig. 1A,
show that while ssDNA did not bind GST protein, it bound GST-X. These
complexes appeared to be specific for ssDNA, since their formation was
competitively prevented by a 100-fold excess of several ssDNA
oligonucleotides with unrelated sequences (Fig. 1A,
lanes 4-10) but not by a double-stranded (ds) DNA
(lane 11). This is in agreement with the previous results of
others showing that HBx does not bind dsDNA (Rossner (1992) and
references therein). The ssDNA-HBx complex was further retarded in the
presence of anti-HBx serum, indicating that HBx is a component of that
complex (lane 12). Together, these results suggest that HBx
interacts with ssDNA in a manner that is non-sequence-specific.
Fig. 1.
HBx interacts with ssDNA in a manner that is
not sequence-specific. A, electrophoretic mobility shift
assay (EMSA) of HBx-ssDNA interactions in the presence of
oligonucleotide competitors. Lane 1, free probe; lane
2, 0.3 µM GST; lanes 3-12, 91 nM GST-X. Lanes 4-10, a 100-fold excess of
unlabeled competitor single-stranded oligonucleotides; lane
11, supercoiled plasmid pGEM3 DNA; lane 12, anti-HBx
serum. B, UV cross-linking of HBx with ssDNA. Lane
1, no protein; lane 2, GST; lanes 3-7,
GST-X. The dsDNA and ssRNA competitors are as indicated (lanes
4-7). C, [35S]HBx binding to
ssDNA-agarose beads. HBx was translated in rabbit reticulocyte lysates
in vitro in the presence of [35S]methionine
from pSPX. Lanes 1-3 represent an input (1:20) of the
following: in vitro synthesized basal transcription factor
TFIIB (lane 1), unprogrammed rabbit reticulocyte lysates
with [35S]methionine (lane 2), and HBx
(lane 3). The ssDNA-agarose bound TFIIB (lane 4),
unprogrammed lysates (lane 5), and HBx (lane 6).
D, HBx binds to the single-stranded region of native HBV
DNA. EMSA of HBx-ssDNA interactions in the presence of a
phenol-extracted genomic HBV and filled-in DNA is shown. Lane
1, free probe; lane 2, GST; lanes 3-8,
GST-X. Lanes 4-8, in the presence of competitor HBV native
DNA (lane 4); HBV filled-in DNA (lane 5); M13
ssDNA (lane 6), and M13 filled-in DNA (lane 7).
HBV and M13 DNAs were filled in with reverse transcriptase, and then
0.1 units of mung bean nuclease was added to remove any residual
unfilled ssDNA. 10 ng of HBV and M13 DNAs were added as competitor.
E, E. coli SSB competes with HBx for ssDNA
binding. Lane 1, no protein; lane 2, GST;
lanes 3-6, GST-X. This is shown in the presence of
increasing amounts (26, 52, and 260 nM) of E. coli SSB (lanes 4-6, respectively). Lanes
3-6 contain 100 ng of GST-X. F, UV cross-linking of
HBx-ssDNA. Lane 1, no protein; lane 2, GST;
lanes 3-6, GST-X. This is shown in the presence of
increasing amounts (26, 52, and 260 nM; lanes
4-6, respectively) of E. coli SSB. Lanes
3-6 contain 91 nM GST-X.
In the next experiment, we examined the direct binding of HBx to ssDNA
by the UV cross-linking method. A 32P-labeled ssDNA
oligonucleotide probe was mixed with either GST or GST-X proteins and
UV-cross-linked (Fig. 1B). GST protein was not cross-linked
to the probe (lane 2). A radiolabled GST-X protein band of
approximately 64 kDa, which represents GST-X protein cross-linked to
the 32P-labeled probe, was fractionated by SDS-PAGE
(lane 3). The 32P-labeled probe migrated as a
20-kDa band in the SDS gel as seen in lane 1 and other
lanes. Further competition with unlabeled dsDNA and RNA in the UV
cross-linking experiment confirms the specificity of HBx interaction
with ssDNA (lanes 4-7). It should be noted here that the
E. coli SSB protein migrates at about 19 kDa on SDS-PAGE and
does not fall within the range of 44-65-kDa proteins, which allays the
concern of a contamination of ssDNA binding activity from bacterial
extracts in UV cross-linking experiments. In summary, the results
obtained by both mobility shift assays and UV cross-linking method
indicate that HBx interacts with ssDNA and RNA. Characterization of
HBx's interactions with RNA will be described elsewhere.
To provide an alternate source of HBx for binding studies, the
X-protein was synthesized in rabbit reticulocyte lysates in the
presence of [35S]methionine. The in vitro
synthesized [35S]HBx was allowed to interact with
single-stranded DNA-agarose beads (Fig. 1C, lane
6). After extensive washing, the mixture was fractionated by 13%
SDS-PAGE. The results show that HBx bound to the ssDNA-agarose beads
(lane 6). As a positive control, the basal transcriptional
factor TFIIB was included (lane 4). TFIIB has been
previously shown to bind single-stranded DNA. Unprogrammed lysates do
not show a ssDNA binding protein (lane 5). These results
together show that HBx, irrespective of the source, displayed affinity
for single-stranded nucleic acids.
The genomic HBV DNA within the virions is partially double-stranded,
containing a substantial single-stranded DNA region. Most experimental
approaches require the disruption of virions in order to observe
HBx-ssDNA interactions. Chaotropic agents will likely lead to the
dissociation of HBx-ssDNA complexes. With this caveat in mind, we have
used phenol-extracted HBV genomic DNA as a competitor in a mobility
shift assay to demonstrate that HBx can associate with the ssDNA region
of the genomic HBV DNA (Fig. 1D, lane 4). HBV DNA
filled in with reverse transcriptase did not compete in this assay
(lane 5). The rationale of using HBV DNA (in native
conformation and filled in) is only to indicate the specificity of HBx
in binding the single-stranded region of the DNA. These results by no
means suggest that HBx is associated with the native HBV DNA in the
virions. These studies are currently in progress. Filamentous
bacteriophage M13, mp18 ssDNA, and filled in dsDNA were used as
controls (lanes 6-7).
In the next analysis, purified E. coli single-stranded DNA
binding protein (E. coli SSB) was used to investigate its
ability to displace HBx-ssDNA complexes. The E. coli
SSB protein is a stable homotetramer and binds to ssDNA nonspecifically
(Lohman and Ferrari (1994) , and references therein). In a
competition analysis, E. coli SSB competed with HBx for
binding to ssDNA (Fig. 1E, lanes 4-6). These
results were further confirmed by the UV cross-linking experiment shown
in Fig. 1F (lanes 4-6). In this respect, HBx
differs from other sequence-specific mammalian SSB proteins whose
interaction with ssDNA is not displaced by E. coli SSB in
competition experiments. These results further support the idea that
HBx binds to ssDNA without sequence specificity.
Time Course of HBx-ssDNA Complex Formation
To determine the
association time of HBx-ssDNA complexes, incubations were performed at
various lengths of time at 30 °C (Fig.
2A). The results of the electrophoretic
mobility shift assay revealed that the minimum time period required for
HBx to interact with ssDNA was 2.0 min (lane 7). After
longer exposure (5 days), faint HBx-ssDNA complexes were observed in
lanes 4-6 in contrast to the overnight exposure of the gel
shown in Fig. 2A (data not shown). Incubation at 3, 4, 5, 10, 20, 30, and 60 min did not result in a change in the intensity of
the HBx-ssDNA complex band (lanes 8-14). GST alone did not
interact with the radiolabeled single-stranded DNA probe (lane
2). Together, these results show that most of the HBx-ssDNA
complexes are formed approximately within 2 min and are stable for at
least up to 60 min.
Fig. 2.
The association time and estimation of
optimal pH for HBx-ssDNA interactions. A, EMSA of HBx-ssDNA
interactions at various time points. Lane 1, free probe;
lane 2, GST; lanes 3-14, GST-X. In lanes
3-14, incubation was carried out at 0.5, 0.7, 1, 1.5, 2, 3, 4, 5, 10, 20, 30, and 60 min, respectively. B, EMSA of HBx-ssDNA
interactions at various pH values. Lane 1, free probe;
lane 2, GST; lanes 3-20, GST-X. The pH of
incubation buffer is indicated above each
lane.
Effect of pH Variation on HBx-ssDNA Interactions
HBx
interactions with ssDNA were examined at varying pH, ranging from 3 to
12. The EMSA results show that HBx did not interact with ssDNA at pH 3 and 3.5 (Fig. 2B, lanes 2 and 3). The
affinity for HBx to interact with ssDNA was reduced between pH 4 and
6.5 (lanes 4-9). Maximal interactions occurred between pH
7.5 and 11 (lanes 10-16). At pH higher than 11, the
interaction was considerably reduced (lanes 17-18). The
observation that the complex is most stable between pH 7.5 and 11 suggests that amino acid side chains such as lysine may be involved in
the binding; the pKa for the lysine side chain is
10.53 in the free amino acid. It is possible that the pH stability of
the HBx-ssDNA interactions reflect the requirement for lysine to be
protonated for complex formation. The weak HBx-DNA interactions at the
pH extremes are likely due to protein denaturation.
Effect of Mono- and Divalent Cations on HBx-ssDNA
Interactions
The HBx-ssDNA interaction studies were conducted in
the absence and presence of various concentrations of KCl, NaCl, and
MgCl2 (Fig. 3). Although MgCl2
is not required for the HBx-ssDNA interaction, tighter binding was
observed at low MgCl2 concentrations compared with NaCl or
KCl. Note the absence of free DNA at low concentrations of
MgCl2 (compare lanes 3-9 in Fig. 3C
with lanes 2-4 in Fig. 3, A and B).
It is possible that the observed tighter binding in the presence of low
MgCl2 concentrations is due to preferential
Mg2+ binding by the complex. At higher MgCl2
concentrations, weaker binding was observed. Above 100 mM
MgCl2 concentration, an abrupt decrease in binding was
observed, and a higher molecular weight complex is clearly visible in
the wells. Higher concentrations of MgCl2 may promote
protein aggregation.
Fig. 3.
Requirements of mono- or divalent cations for
HBx-ssDNA interactions. A, effect of NaCl. Lane
1, free probe; lanes 2-14, GST-X. In lane
2, the incubation was done without any mono- or divalent cations
(i.e., NaCl, KCl, or MgCl2). In lanes
3-14, increasing concentrations of NaCl were added as follows: 25 mM (lane 3), 50 mM (lane
4), 75 mM (lane 5), 100 mM
(lane 6), 150 mM (lane 7), 200 mM (lane 8), 300 (lane 9), 400 mM (lane 10), 500 mM (lane
11), 700 mM (lane 13), and 800 mM (lane 14). B, effect of KCl.
Lane 1, free probe; lanes 2-18, GST-X. In
lane 2 the incubation was done without any mono- or divalent
cations. In lanes 3-18, increasing concentrations of KCl
were added as follows: 25 mM (lane 3), 50 mM (lane 4), 75 mM (lane
5), 100 mM (lane 6), 150 mM
(lane 7), 200 mM (lane 8), 300 mM (lane 9), 400 mM (lane
10), 500 mM (lane 11), 600 mM
(lane 12), 700 mM (lane 13), 800 mM (lane 14), 900 mM (lane
15), 1000 mM (lane 16), 1200 mM
(lane 17), and 1500 mM (lane 18).
C, MgCl2. Lane 1, free probe;
lane 2, GST; lanes 3-14, GST-X. In lane
3 the incubation was done without any mono- or divalent cations.
In lanes 4-14 increasing concentrations of
MgCl2 were added as follows: 1 mM (lane
4), 2 mM (lane 5), 5 mM
(lane 6), 10 mM (lane 7), 25 mM (lane 8), 50 mM (lane
9), 100 mM (lane 10), 150 mM
(lane 11), 200 mM (lane 12), 250 mM (lane 13), and 300 mM (lane
14).
The data described in Fig. 3 clearly show that the HBx-ssDNA
interaction decreased with increasing divalent and monovalent salt
concentration, consistent with the predicted behavior for protein-DNA
interactions (Record et al., 1976 , 1978 ). A higher [KCl]
was required to abolish binding relative to [NaCl]; no binding was
detected at 800 mM NaCl compared with 1500 mM
KCl. These results suggest that preferential interaction of HBx with
K+ may accompany binding. In addition, MgCl2
was effective at disrupting the HBx-ssDNA complexes at much lower
concentration (300 mM; Fig. 3C,
lane 14) compared with the monovalent salts (1500 mM KCl (Fig. 3A, lane 18) and 800 mM NaCl (Fig. 3, lane 14)). These properties are
consistent with the expected salt dependence associated with
protein-ssDNA interactions (Record et al., 1976 , 1978 ).
Fig. 4.
Effect of heparin, cardiolipin, and DTT on
HBx-ssDNA interactions. A, EMSA of HBx-ssDNA interactions in
the presence of heparin. Lane 1, free probe; lanes
2-10, GST-X. 0.1, 1, 5, 10, 25, 50, 100 and 200 mM
heparin was added in lanes 3-10, respectively.
B, EMSA of HBx-ssDNA interactions in the presence of
cardiolipin. Lane 1, free probe; lane 2, GST,
lanes 3-10, GST-X. 1, 5, 10, 25, 50, 100, and 200 mM cardiolipin was added in lanes 4-10,
respectively. C, EMSA of HBx-ssDNA interactions in the
presence of DTT. Lane 1, free probe; lanes 2-10,
GST-X. 0.1, 1, 5, 10, 25, 37.5, 50, 75, and 100 mM DTT with
the final concentration was added in lanes 2-10,
respectively.
Heparin and Cardiolipin Do Not Affect HBx-ssDNA
Interactions
Heparin is a glycosamino glycan containing a
negatively charged carboxylate or a sulfate group and has been
frequently used as a competitor for DNA in protein-DNA binding studies.
Heparin is dissimilar in structure to DNA. It has therefore been used
to investigate protein-nucleic acid complex stability (i.e.,
phosphate backbone versus DNA base interactions). Heparin
was tested for its ability to compete with ssDNA for HBx binding. A
decrease in binding was observed with increasing heparin concentration
up to 200 mM (Fig. 4A, lane 10).
However, heparin was not able to completely compete with DNA,
suggesting that significant nonelectrostatic interactions contribute to
the DNA-HBx complex stability. Cardiolipin is a diphosphatidyl glycerol
containing two negatively charged phosphate groups. When cardiolipin
was used as a competitor in EMSA, similar results were obtained (Fig.
4B).
Effect of DTT on HBx-ssDNA Interactions
The ability of the
reducing agent dithiothreiotol (DTT) to affect the stability of
HBx-ssDNA interactions was determined by incubating the HBx with ssDNA
at increasing concentrations of DTT (0.1-100 mM) (Fig.
4C, lanes 2-10). It was observed that at up to 5 mM DTT, the HBx-ssDNA interactions were not affected
(lane 5). However, DTT concentrations of 10 mM
and above had an inhibitory effect on these interactions (lanes
6-8). The HBx used in this experiment was purified in the
presence of a very low concentration of DTT (0.1 mM);
therefore, the observed HBx-ssDNA complexes seem to be weaker in
comparison with other experiments (Fig. 4, A and
B). It is likely that during the preparation of HBx, some of
its DNA binding activity was lost due to oxidation of the protein. We
conclude that reduced thiol groups are involved in the binding activity
of HBx to ssDNA, probably through stabilization of the correct
conformation of the protein.
Thermostability of HBx-ssDNA Complexes
Effect of temperature
on HBx-ssDNA interaction was investigated by incubating the reaction
mixture at various temperatures (Fig. 5).
Significant binding is observed between 20 and 45 °C. A fraction
(~20%) of ssDNA probe did not bind HBx at 4 °C (lane
3). At 65 °C only a small fraction (~5%) of the HBx-ssDNA
complex was stable (lane 8).
Fig. 5.
Thermostability of HBx-ssDNA
interactions. EMSA of HBx-ssDNA interactions at various
temperatures. Lane 1, free probe; lane 2, GST;
lanes 3-8, GST-X. The incubation temperatures were as
follows: 4 °C (lane 3), 20 °C (lane 4),
30 °C (lane 5), 37 °C (lane 6), 45 °C
(lane 7), and 65 °C (lane 8).
Titration of HBx with ssDNA
HBx was added in increasing
concentrations (5-100 ng; 0.09-90 nM) to a constant
amount of radiolabeled DNA (0.1 ng; 0.484 nM) (Fig.
6). The single-stranded DNA oligonucleotide probe
representing the nucleotide 1125-1150 sequences of the enhancer I
region of HBV genome was radiolabeled at the 5 end by T4
polynucleotide kinase in the presence of [ -32P]ATP.
The HBx concentration required to bind half of the DNA was
approximately 90 nM, determined from PhosphorImager
analysis from EMSA gels. We emphasize that this value is only an order
of magnitude estimate for the dissociation constant. We note that these
titrations were performed with the bacterially expressed GST fusion
protein and may vary with a purified and unfused HBx. In our experience
with the Studier's pET expression system in which the X-gene is not
fused to any moiety, HBx formed inclusion bodies (Jameel et
al., 1990 ). Denaturation of these complexes uniformly produced
functionally inert HBx molecules, perhaps due to malfolding. GST-X
fusion protein on the other hand produced soluble protein and hence has
been used extensively for in vitro analyses.
Fig. 6.
Affinity of HBx for ssDNA. EMSA of
HBx-ssDNA interactions in the presence of increasing amounts of HBx.
Lane 1, free probe; lanes 3-10, with GST-X.
Increasing concentrations of GST-X were added as follows: 0.1 ng, 0.09 nM (lane 2); 0.5 ng, 0.45 nM
(lane 3); 5 ng, 4.5 nM (lane 4); 12.5 ng, 11 nM (lane 5); 25 ng, 22 nM
(lane 6); 37.5 ng, 34 nM (lane 7); 50 ng, 45 nM (lane 8); 75 ng, 68 nM
(lane 9); and 100 ng, 91 nM (lane
10).
Determination of Base Specificity of HBx-ssDNA
Interactions
The base specificity of the HBx-ssDNA interaction
was investigated by performing EMSA in the presence of varying
concentrations (0.1, 1, 5, 10, 50, 100, 500, and 1000 ng) of competitor
homopolymer oligonucleotides. These are as follows; d(A)25
(Fig. 7A), d(G)25 (Fig.
7B), d(C)25 (Fig. 7C), and
d(T)25 (Fig. 7D). The results described in Fig.
7 show that polypyrimidines d(C)25 and
d(T)25 were more effective competitors than polypurines
d(A)25 and d(G)25. Even in the presence of a
molar excess of cold oligonucleotides (d(A)25 and
d(G)25) very little effect of competitor oligonucleotides
was seen on the formation of the HBx-ssDNA complex (Fig. 7,
A and B, lanes 9 and 10).
These results suggest that HBx shows a preference for pyrimidine
residues during its binding to ssDNA. Similar base preferences have
been observed with other single-stranded DNA binding proteins (Lohman
and Ferrari, 1994 ; Kim et al., 1992 ).
Fig. 7.
Determination of base specificity of
HBx-ssDNA interactions by using poly d(A)25,
d(C)25, d(G)25, and d(T)25.
EMSAs are shown of HBx-ssDNA interactions in the presence of
oligopurines d(A)25 (A), d(G)25
(B), and oligopyrimidines d(C)25 (C),
and d(T)25 (D). Lane 1, free probe
(0.1 ng); lanes 2-10, GST-X. In all cases, lanes
3-10 contain 0.1, 1, 5, 10, 50, 100, 500, and 1000 ng of the
competitor oligonucleotides, respectively.
DISCUSSION
The mechanism(s) by which HBx transactivates gene expression is a
subject of intense investigation. Its inability to bind cis-acting
regulatory DNA elements has been well documented (reviewed by Rossner
(1992) and references therein). In this report, we present evidence
that HBx interacts with ssDNA in a manner that is not
sequence-specific. The experimental approaches used include mobility
shift assay, UV cross-linking of HBx with ssDNA, and direct retention
of HBx on a single-stranded DNA agarose column. We have conducted a
series of experiments relating to the various biochemical parameters of
HBx-ssDNA interactions. These studies indicate that HBx displays
characteristics that are similar to those known for other viral and
cellular SSB proteins. HBx binds preferentially to single-stranded
nucleic acids and fails to bind dsDNA. Although HBx does not bind to
ssDNA sequence with any specificity, it does show some base specificity
of binding, i.e. d(T)25 and d(C)25
are more effective at competing with ssDNA for binding than
d(A)25 and d(G)25. This kind of base
specificity has been observed for other SSBs (Lohman and Ferrari, 1994 ;
Kim et al., 1992 ).
The determination of the heat stability of the HBx binding revealed
that HBx-ssDNA interactions are stable at 45 °C. Other proteins that
have been shown to remain stable in complex with DNA at elevated
temperatures include basal transcription factor TFIIA at 55 °C
(Waldschmidt and Seifart, 1992 ), TFIID at 47 °C (Nakajima et
al., 1988 ), and mammalian transcription factor PBP binding to U6
genes at 43 °C (Wanandi et al., 1993 ). At pH 11, the
HBx-ssDNA interaction was fairly stable, which suggests a potential
role of lysine residues in these interactions. In the presence of 10 mM DTT or greater, HBx-ssDNA interactions were abolished.
This is likely a result of the disruption of Cys-Cys interactions in
the protein necessary to maintain a properly folded structure. Our
future work will be directed toward altering these residues by
site-directed mutagenesis to identify the regions of HBx critical for
its interactions within ssDNA.
The single-stranded DNA- or RNA-binding proteins play significant roles
in DNA repair, replication, and recombination (Hoeijimakers (1991),
Challberg and Kelly (1989) , Lohman and Ferrari (1994) , and references
therein). SSBs can also act as DNA-binding stimulatory factors. One
such protein, a 45-kDa DNA-binding stimulatory factor isolated from
yeast, has been shown to promote binding of the purified oestrogen
receptor to its responsive element (Mukherjee and Chambon, 1990 ). FBP
is an another example of a sequence-specific, single-stranded DNA
binding protein which has been shown to activate the upstream element
at the FUSE site of the c-myc gene (Duncan et
al., 1994 ). This activity would be consistent with previous
observations relating to HBx's ability to induce the DNA binding
specificity of ATF-2/CREB and c-Jun·c-Fos heterodimers to their
respective sequence motifs (Maguire et al., 1991 ; Natoli
et al., 1994 ). Confirming these binding properties, a recent
report demonstrates that in the presence of HBx, the binding
specificity of CREB (KD = 10 7
M) with the HBV CRE motif within the enhancer I element
increased by an order of magnitude (KD = 10 8 M) (Williams and Andrisani, 1995 ).
HB virion DNA is partially double-stranded with a variable length of
single-stranded region. The unusual and unique nature of native virion
DNA is the result of incomplete DNA synthesis in the viral core
particles. Whether HBx is bound to the single-stranded region of the
native genomic HBV DNA is an interesting question that needs to be
investigated. In the context of HBV life cycle, HBx may be implicated
in binding to the ssDNA region of the genomic DNA and perhaps
pregenomic RNA during precore assembly. The data presented here suggest
that HBV transactivator protein, HBx, can bind to single-stranded DNA
in vitro. Our future studies will focus on defining in
greater detail the exact role of HBx in the context of the HBV life
cycle. Several eukaryotic DNA viruses encode single-stranded DNA
binding proteins that bind to ssDNA. These include SV40 T antigen
(Stahl et al., 1986 ), herpes simplex virus 1 ICP8 and UL9
(Olivo et al., 1988 ), adenovirus DBP (p72) (Challberg and
Kelly, 1989 ), and Autographa californica nuclear
polyhedrosis virus Lef-3 (Hang et al., 1995 ). The role of
these proteins have been documented in DNA replication (Challberg and
Kelly, 1989 ). The A. californica nuclear polyhedrosis virus
Lef-3 protein has been shown to play a role in late and very late gene
expression.
A wealth of information is available on the biochemical properties of
bacterial single-stranded DNA or RNA binding proteins (SSBs). SSBs play
significant roles in transcription, DNA repair, replication, and
recombination (Hoeijmakers, 1993 ; Challberg and Kelly, 1989 ; Lohman and
Ferrari, 1994 ). In its newly assigned role as a viral SSB, one possible
function of HBx could be to bind melted template and prevent
reannealing during transcription and perhaps other cellular processes
where such a function is required. The single-stranded DNA binding
activity of HBx may also have an impact on other important cellular
functions such as DNA repair. Support for HBx's role in DNA repair
comes from a recent report, in which HBx was shown to interact with
UV-damaged DNA repair enzyme (Lee et al., 1995 ). Another
possible physiological relevance of single-stranded DNA binding
property of HBx could be envisioned during transcription initiation. We
have recently shown that HBx can interact with TBP, a principal
component of TFIID (Qadri et al., 1995 ) and components of
TFIIH.2 HBx-TBP and HBx-TFIIH interactions may provide
access for HBx to the melted template, where it can bind to the
denatured DNA strand and contribute to the stability of preinitiation
complex assembly process.
Our future investigations will be focused on elucidating the biological
and functional relevance of HBx-ssDNA interactions. This report, which
defines the biochemical criteria of HBx-ssDNA interactions, constitutes
the first step toward that goal. These biochemical parameters would be
useful in designing strategies in recovering HBx-genomic DNA complexes
from HBV particles and in conducting analyses of interactions between
HBx and cellular targets in vitro. Further, these studies
have the potential to provide clues to its fundamental role in viral
and cellular processes and contribute to the understanding of the exact
mechanism(s) by which HBx may accomplish its regulatory functions.
FOOTNOTES
*
This work was supported by grants from the National
Institute of Health, American Cancer Society, and Lucille P. Markey
Charitable Trust (to A. S). 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.
Recipient of a fellowship from an American Cancer Society
institutional grant.
¶
To whom correspondence should be addressed: Dept. of
Microbiology, Program in Molecular Biology, University of Colorado,
Health Sciences Center, B 172, 4200 E. 9th Ave., Denver, CO 80262. Tel.: 303-270-7016; Fax: 303-270-8330.
1
The abbreviations used are: HBV, hepatitis B
virus; TBP, TATA-binding protein; ERCC, excision repair
cross-complementing; TFIIA, -B, -D, and -H, transcription factor IIA,
-B, -D, and -H, respectively; TEMED,
N,N,N ,N -tetramethylethylenediamine
SSB, single-stranded DNA-binding protein; ssDNA, single-stranded
DNA; dsDNA, double-stranded DNA; PMSF, phenylmethylsulfonyl fluoride;
PAGE, polyacrylamide gel electrophoresis; GST, glutathione
S-transferase; EMSA, electrophoretic mobility shift
assay.
2
I. Qadri, J. W. Conaway, R. C. Conaway, and A. Siddiqui, submitted for publication.
Acknowledgments
We thank Dr. D. Reinberg for providing the
TFIIB construct for in vitro translation and Dr. C. McHenry
for providing the E. coli SSB protein.
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