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Journal of Virology, May 2003, p. 5512-5518, Vol. 77, No. 9
0022-538X/03/$08.00+0 DOI: 10.1128/JVI.77.9.5512-5518.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.
Department of Biological Sciences, Boehringer Ingelheim (Canada) Ltd., Laval, Canada H7S 2G5
Received 26 September 2002/ Accepted 3 February 2003
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FIG. 1. Purified proteins used in this study. (A) Schematic diagram of the 708-amino-acid SV40 large T antigen. The position of the OBD, located between amino acids 131 and 260, is indicated relative that of other functional domains including the J domain (J), the ATPase domain and the zinc finger domain (Zn). Regions of the protein involved in binding to the cell cycle regulatory protein Rb and p53 are indicated as black bars. (B) Sodium dodecyl sulfate-15% polyacrylamide gel electrophoresis of purified proteins stained with Coomassie blue. Aliquots (3 µg) of full-length large T antigen, of polyhistidine-tagged OBD (His-OBD), and of the corresponding GST fusion protein (GST-His-OBD) were analyzed. Concentrations of the His-OBD and Gst-His-OBD proteins were estimated by absorbance at 280 nm in 6 M guanidine hydrochloride using the following molar extinction coefficients: His-OBD = 9,320 M-1cm-1; GST-His-OBD = 50,480 M-1cm-1. The concentration of full-length T antigen was determined by Bradford analysis. (C and D) Gel filtration profiles of His-OBD (C) and Gst-His-OBD (D) proteins. His-OBD (75 µg) and GST-His-OBD (150 µg) were chromatographed on a Superdex 75 PC 3.2/3.0 and a Superdex 200 PC 3.2/3.0 gel filtration column, respectively, using the SMART system (Pharmacia) in a solution containing 25 mM Tris (pH 8.0), 100 mM NaCl, 1 mM EDTA, 1 mM dithiothreitol, 10% glycerol. Molecular mass standards in (C) were blue dextran (2,000 kDa), albumin (67.0 kDa), ovalbumin (43.0 kDa), chymotrypsinogen A (25.0 kDa), and RNase A (13.7 kDa). These standards were chromatographed in two groups to increase peak resolution; both elution profiles are superimposed in the figure. Molecular mass standards in panel D were thyroglobulin (670 kDa), gamma globulin (158 kDa), ovalbumin (44 kDa), myoglobin (17 kDa), and vitamin B12 (1.35 kDa). The positions of each standard and of the void volume (V0) are indicated by black triangles. The molecular masses of the His-OBD and of GST-His-OBD proteins calculated from their retention times relative to those of the standards are 15.8 and 92 kDa, respectively. These values are consistent with the His-OBD and of GST-His-OBD proteins being primarily monomeric and dimeric, respectively (molecular mass of a monomer calculated from the primary amino acid sequence is 16.0 kDa for His-OBD and 42 kDa for Gst-His-OBD).
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)sample/(I|| + 2I
)free, where I|| and I
are the parallel and perpendicular fluorescence intensities respective to the orientation of the excitation polarizer. Finally the fraction of bound probe was plotted versus the concentration of free protein and the resulting isotherms were fitted by nonlinear least-squares regression with the program GraFit 3.09b (Erithicus Software Ltd.) to the equation describing the following tight binding equilibrium, D + E
DE (D = duplex DNA; E = T-antigen OBD; DE = DNA-OBD complex): fraction bound (FB) = [(DT + ET + Kd) - {(DT + ET + Kd)2 - (4DTET)}1/2]/(2DT) where total concentrations of T-antigen OBD and fluorescent probe are defined by ET and DT. Duplicates of each binding reaction were prepared in a 96-well plate format and three readings registered on a Victor 2 Multilabel HTS Counter (Wallac) using a 480/535 nm excitation/emission filter set. All sample measurements were corrected for blank fluorescence (buffer only). From the binding isotherms in Fig. 3, dissociation constants of 31 and >1,000 nM were obtained for the binding of the OBD to the TBS probe and the control probe, respectively, and dissociation constants of 1.5 and >1,000 nM were obtained for the binding of GST-His-OBD to the TBS probe and the control probe, respectively.
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FIG. 2. DNA duplexes used in this study. (A) Fluorescent probes and analogous competitor oligonucleotides. The sequences of the fluorescein (F)-labeled strand of the probe containing a single T antigen-binding site (TBS) and of the control probe are indicated. Similarly, the top strand of competitor oligonucleotides containing one, two, or no TBS is indicated. TBS are boxed in black. (B) Oligonucleotides derived form the SV40 origin. The sequence of the 64-bp double-stranded core origin is indicated. The AT-rich and early palindrome regions are boxed. The positions of site II and of the four pentanucleotide TBS are indicated. The bottom of the figure describes the sequence of the top strand of competitor oligonucleotides derived from the 31-bp site II or from the 64-bp core origin. Functional (not mutated) TBS are boxed in black and their numbers are specified in the nomenclature of each oligonucleotide. Site II oligonucleotides in which the spacer region between TBS 1 and 3 has been increased by 1, 2, or 3 bp are referred to as +1, +2, and +3, respectively.
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FIG. 3. DNA-binding activity of the large T-antigen OBD and of full-length large T antigen detected by fluorescence anisotropy. Binding isotherms were generated with purified His-OBD (A) or GST-His-OBD (B) at room temperature in binding buffer (50 mM Tris [pH 7.6], 0.005% NP-40, 1 mM EDTA, 1 mM dithiothreitol) containing 100 mM NaCl and a 15 nM concentration of either a one-TBS-containing probe (circles) or a control probe lacking any TBS (triangles). Binding isotherms generated with large T antigen (C and D) were obtained at room temperature in binding buffer containing the indicated concentration of NaCl and either a one-TBS-containing probe (C) or a control probe lacking any TBS (D).
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I + E + D
DE. By this method, the Ki of the His-OBD was found to be 28 nM for the duplex containing a single TBS and >924 nM for the one devoid of TBS (Table 1). These Ki values are in close agreement to the Kd values determined from direct binding to fluorescent probes, suggesting that the fluorescein moiety does not substantially affect binding. |
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TABLE 1. Ki for His- and GST-His-OBD and IC50 for T antigena
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We were surprised by the findings presented above since we expected that dimerization of the T-antigen OBD would increase substantially its affinity for DNA, as we have observed for the related DBD of the papillomavirus E1 helicase (26). As a control experiment to verify that dimerization of the T-antigen OBD would indeed increase its affinity for DNA, we performed binding experiments with the GST-His-OBD fusion protein. In this protein context the OBD is artificially dimeric (Fig. 1D) because GST itself is a dimer. In experiments measuring the direct binding of GST-His-OBD to fluorescent probes (Fig. 3B), or in competition experiments (Table 1), this protein was found to bind DNA in a sequence-specific manner with an approximately 15-fold-higher affinity for a single TBS than the monomeric OBD. Furthermore, its affinity for two TBS, or for site II and the core origin, was approximately 50-fold higher than that of the monomeric OBD. As expected, the GST-His-OBD fusion proteins showed a substantially higher affinity for pairs of pentanucleotides relative to the corresponding single sites. For example, its affinity for the combination of sites 2 and 4 (Ki = 1.0 nM) was approximately 10-fold higher that its affinity for site 2 (Ki = 11 nM) or site 4 (Ki = 8 nM). This is in contrast to the monomeric His-OBD, which showed only a two- to threefold-higher affinity for sites 2 and 4 (Ki = 62 nM) than for any of these two individual sites (site 2 Ki = 150 nM, site 4 Ki = 123 nM). Collectively, these results indicate that artificial dimerization of the OBD by fusion with GST does increase its affinity for two TBS. From these results one might expect that dimerization of the monomeric OBD, if it were strong, should increase substantially its affinity for two TBS relative to one. Since this was not observed, we surmise that the OBD does not dimerize upon binding to DNA, or dimerizes only weakly, but rather binds primarily in an independent manner to each TBS under our assay conditions. On the basis of these results, we suggest that the OBD dimer observed in EMSA (15) was formed predominantly by the independent binding of two OBD molecules to two adjacent inverted pentanucleotides. Their subsequent cross-linking would have generated an artificial dimer whose higher affinity for site II would have allowed it to resist the harsh conditions of EMSA. In support of this suggestion we verified that artificial dimerization of the OBD, in our case by fusion with GST, does increase its affinity for pairs of binding sites. The fact that cross-linking was essential to observe binding of the ODB to pairs of binding site in EMSA and that binding to a single site could not be observed even with cross-linking (15) further supports our suggestion.
For comparison with the OBD, we performed binding studies with full-length T antigen immunopurified as described previously (24) from baculovirus-infected insect cells (Fig. 1B). The experiments with the isolated OBD were performed in buffer containing 100 mM NaCl so we first attempted to detect binding of full-length T antigen to fluorescent probes under the same salt condition. As can be seen in Fig. 3C and D, T antigen was able to bind to the TBS-containing probe in a sequence-specific manner but with a lower affinity than that of the OBD. In an attempt to increase binding of T antigen to the probe, we performed binding isotherms at lower salt concentrations, either 25 or 50 mM NaCl, or in absence of NaCl. As expected, binding to the TBS-containing probe (Fig. 3C) and to the control probe (Fig. 3D) was increased at lower salt concentrations. We chose to perform all subsequent experiments at 50 mM NaCl since at this concentration binding of T antigen to the TBS-containing probe was increased while binding to the control-probe remained low. Under these conditions, binding of T antigen was sufficiently weak that saturation of the TBS-containing probe could not be reached at the highest protein concentration tested. This prevented us from obtaining a Kd and consequently from calculating Ki values in subsequent competition experiments. Nevertheless, it was still possible to compare the affinities of T antigen for different duplex DNA carrying one, two, or no TBS, or for site II and the core origin by comparing the IC50 of each competitor (Table 1). IC50 values were determined both in absence or presence of ADP-Mg in the binding reactions. ADP was used instead of ATP because ADP can promote assembly of hexamers and double hexamers, but unlike ATP, it does not support DNA unwinding which would complicate interpretation of the results (8, 21). Several observations were made. First in the absence of ADP-Mg, T antigen bound with a comparable affinity to a competitor 24-bp duplex carrying two TBS (IC50=60 nM) as to one carrying a single TBS (IC50=53 nM). Similar results were also obtained with the 31-bp site II oligonucleotide. In this case binding to pentanucleotide pairs 1 and 3 or 2 and 4 was approximately 2.5 to 3.5 times stronger than to the corresponding individual sites in absence of ADP-Mg. Furthermore the affinity of T antigen for binding sites 1 and 3 decreased by less than twofold when the spacing between both sites was increased by 1 to 3 bp (Table 1). These results are consistent with the notion that full-length T antigen binds primarily in an independent manner to all four binding sites within the 31-bp site II oligonucleotide, similarly to what we observed for the isolated OBD.
When the experiments described above were repeated in presence of ADP-Mg, two main observations were made. First, we found that ADP-Mg increased the affinity of full-length T antigen for the longer core origin by approximately 20-fold but had little effect on the affinity for the 31-bp site II oligonucleotide. Specifically the IC50 of the core origin changed from 19 to 1 nM upon addition of ADP-Mg. Second, ADP-Mg dramatically increased nonspecific binding of T antigen to DNA, as observed for the three control probes lacking any TBS (0 TBS, site II mut, and core mut). ADP-Mg increased nonspecific binding to the mutant site II and the mutant core origin by 50- and >250-fold, respectively. By doing so, ADP-Mg greatly reduced the ability of T antigen to discriminate between wild type and mutant site II or the core origin. For example, the difference in affinity between the wild type and mutant core origin that was >200-fold in absence of nucleotide was reduced to 15-fold in presence of ADP-Mg. A possible mechanism by which ADP-Mg could increase the binding of T antigen to the longer core origin and to nonspecific DNA would be by promoting the oligomerization of the protein and/or the interaction of the C-terminal helicase/ATPase domain with DNA. Consistent with this proposal is the observation that ATP increases the size of the T-antigen footprint on the origin (2, 9). Note that although our results suggest that T antigen binds to its recognition sites primarily in an independent manner in absence of ADP, they do not address whether the increased binding to the core origin and to nonspecific DNA induced by ADP is due to cooperative binding. Although this is a very likely possibility, additional experiments are required to address this question.
Concluding remarks. In this study we found that the T-antigen OBD binds primarily in an independent manner to the four TBS in the SV40 origin. This is in contrast to the related papillomavirus E1 DBD, whose affinity for its cognate origin or for pairs of inverted binding sites is approximately 10-fold higher than that for a single site and is dependent on dimerization of the protein and on having the correct spacing between both binding sites (26). Interestingly, we note that the affinity of the T-antigen OBD for a single TBS (Ki between 57 and 150 nM) is comparable to that of a dimer of the E1 DBD for two E1 binding sites (Ki= 80 nM for the HPV11 E1 DBD at 100 mM NaCl [26]). Therefore, it may be that dimerization is necessary for papillomavirus E1 to form a stable protein-DNA complex at the origin whereas it is dispensable for T antigen.
The affinities measured in this study are consistent with a two-step model of the assembly of T antigen at the origin. In the first step, the T-antigen OBD or the full-length protein in absence of ADP-Mg would bind to all four pentanucleotides in site II, predominantly in an independent manner. It is likely that binding to all four sites is necessary for proper assembly since double hexamers formed on only two of the four TBS, either a combination of sites 1 and 3 or 2 and 4, do not catalyze unwinding (14, 25). Formation of a tetramer of T antigen at the origin would make the T-antigen system similar to that of the related papillomavirus E1 helicase, which was shown to assemble at the origin via a tetrameric intermediate (11). An important difference however would be that formation of the T-antigen tetramer would proceed by the sequential and independent binding of four monomers to the origin, in sharp contrast to the E1 tetramer which is assembled from two independent dimers (11) (Fig. 4).
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FIG. 4. Model for the assembly of SV40 T antigen at the origin and comparison with the assembly of the related papillomavirus E1. (A) Assembly of the T-antigen OBD on site II. The DNA is represented in gray. The four pentanucleotides TBS are indicated by arrows and numbered according to Fig. 2. The figure shows the stepwise, independent binding of four OBD (colored in black) onto the four TBS in site II. Assembly is shown to proceed stepwise starting with binding of the OBD to the highest affinity site (site 3) and ending with binding to the weakest site (site 2). (B) Assembly of the papillomavirus E1 DBD at its cognate origin. The four E1 binding sites found in many papillomavirus origins (4) are indicated by arrows as two overlapping pairs of inverted repeats. Assembly is shown to begin by the binding of a monomer of the E1 DBD (black box) to the highest-affinity binding site, site 4 for HPV11 (26). The affinity of a monomer for the origin is weak (Ki = 850 nM for the HPV11 E1 DBD at 100 mM NaCl [26]), but its binding is increased approximately 10-fold upon dimerization (for a dimer of the HPV11 E1 DBD Ki = 80 nM at 100 mM NaCl [26]). Assembly is shown to proceed via the cooperative binding of two E1 DBD on sites 2 and 4 to form an initial stable dimer. This is followed by the assembly of a second dimer on the weaker affinity sites 1 and 3 (26). A recent crystal structure of the tetrameric E1 DBD-DNA complex revealed that both dimers do not interact with each other significantly (11). The low affinity and specificity of E1 for its target site are such that, in vivo, dimerization of full-length E1 probably occurs only if the protein is recruited to the origin by E2, a transcription/replication factor with high affinity for the origin.
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