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Journal of Virology, January 2003, p. 135-141, Vol. 77, No. 1
0022-538X/03/$08.00+0 DOI: 10.1128/JVI.77.1.135-141.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.
CNRS UMR8532, LBPA, Ecole Normale Supérieure de Cachan, 94235 Cachan,1 Bioalliance Pharma SA, 75015 Paris, France2
Received 18 June 2002/ Accepted 17 September 2002
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The viral genomic clone containing the mutation IN(C280S) was obtained by cloning the EcoRI-NcoI DNA fragment from the pBRU2 viral genomic clone into the pGEM-T vector (Promega). The C280S substitution was constructed as described above and verified by DNA sequencing. The final vector, pBRU2-IN(C280S), was obtained by reinserting the fragment bearing the mutation into pBRU2.
Production and purification of IN. High Five cells (Invitrogen) were infected with recombinant baculoviruses and harvested 45 h later. The cells were washed in ice-cold phosphate-buffered saline and resuspended in ice-cold buffer (20 mM Tris-HCl [pH 8], plus 1 M NaCl supplemented with an antiprotease cocktail) (Roche Diagnostics, Meylan, France). They were lysed in a French press (1,000 lb/in2) and centrifuged (40 min at 12,000 x g and 4°C). The supernatant was filtered (0.45-µm-pore-size filter) and incubated for 2 h with Ni-NTA-agarose beads (Qiagen). The beads were washed twice with 10 volumes of ice-cold buffer A (20 mM Tris-HCl [pH 8,] 1 M NaCl), six times with 10 volumes of buffer A containing 50 mM imidazol, and twice with 10 volumes of buffer A containing 100 mM imidazol. His-tagged IN was then eluted from the beads with buffer A supplemented with 50 µM ZnSO4 and 1 M imidazol. The imidazol was removed by dialysis against a storage buffer containing 20 mM Tris-HCl (pH 8), 1 M NaCl, 50 µM ZnSO4, and 10% (vol/vol) ethylene glycol. The sample was aliquoted and rapidly frozen at -80°C.
IN activity assay. IN activity assays were performed as previously describes (19). Gels were analyzed using a STORM Molecular Dynamics PhosphorImager (Pharmacia Biosciences).
Cells and viruses. All culture media were supplemented with 10% fetal calf serum and penicillin-streptomycin. HeLa and P4 (HeLa-CD4+-ßGal) cells were grown in Dulbecco's minimal essential medium. CEM4fx were grown in RPMI 1640 medium. CEM4fx cells were derived from the human lymphoid cell line CEM (ATCC CCL119) and express high levels of CD4 antigen. Viral stocks were obtained by transfection of HeLa cells with pBRU2 and pBRU2-IN(C280S) using Superfect (Qiagen). Virus was harvested 72 h posttransfection. For infection experiments, CEM4fx or P4 cells or peripheral blood lymphocytes (PBL) were infected with filtered cell-free virus-containing supernatants in 96-well plates at 10,000 cells/well (p24 production). Viral supernatants were removed 2 h after infection. De novo viral production was estimated by the p24 enzyme-linked immunosorbent assay (ELISA) (DuPont-NEN).
Anisotropy decay measurements. Fluorescence experiments were performed as previously described (10, 11). Excitation and emission wavelengths were 298 and 350 nm, respectively. Fluorescence experiments were performed at 25°C in 20 mM Tris-HCl buffer (pH 7.2) containing 200 nM IN, 5 mM MgCl2, and 50 mM NaCl under reducing (5 mM dithiothreitol [DTT]) or nonreducing conditions. Analysis was performed by the maximum-entropy method (3).
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FIG. 1. IN produced in insect cells forms disulfide-linked dimers. (A and B) His-tagged IN was purified by nickel affinity in the absence of a reducing agent and subsequently analyzed by SDS-PAGE in the presence (lanes 1 and 3) or absence (lanes 2 and 4) of 10 mM DTT. (A) Proteins were revealed by silver staining. (B) Proteins were revealed by western blotting using an anti-IN polyclonal antibody. Molecular masses (MW) in kilodaltons are indicated on the left. (C) IN was purified from insect cells and analyzed by SDS-PAGE in the presence (lanes 1 to 3) or absence (lanes 4 to 6) of ß-mercaptoethanol. Various concentrations of the thiol-blocking agent NEM were added before cell lysis. Lanes 1 and 4, no NEM; 2 and 5, 0.5 mM; 3 and 6, 5 mM. Molecular masses in kilodaltons are indicated on the right.
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FIG. 2. Disruption of the disulfide linkage of covalent IN oligomers by mutation of cysteine 280 in vitro and in viral particles. (A) Recombinant mutant proteins were purified in the absence of reducing agents. Equivalent quantities of protein were loaded onto a 10% acrylamide gel in the presence (lanes 1 to 4) or absence (lanes 5 to 8) of 10 mM DTT. Proteins were revealed by silver staining. Molecular weights in kilodaltons are indicated on the left. M, monomer; D, dimer; WT, wild type. (B) Oligomeric status of IN(C280S) in the viral particles. Pelleted virus, corresponding to 75 ng of p24 protein, was lysed in 20 mM HEPES (pH 7.5)-150 mM NaCl-0.5% Triton X-100 buffer in the presence (lanes 1 and 3) or absence (lanes 2 and 4) of 50 mM DTT. Lysed virions were analyzed by electrophoresis on a 10% acrylamide gel and revealed by Western blotting using polyclonal antibodies against IN. Molecular masses in kilodaltons are indicated on the left. wt, wild type.
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Cysteine 280 is responsible for the disulfide bridging in vitro. IN encoded by the genomic clone HBX2 contains six cysteine residues scattered among the three domains of the protein: two in the N-terminal domain at positions 40 and 43; three in the catalytic core domain at positions 56, 65, and 130; and one in the C-terminal domain at position 280. To identify the cysteine residues engaged in disulfide bridges, four of the six cysteines were mutated into serines. Residues C40 and C43 of the N-terminal domain were not studied: there is structural and biochemical evidence that they are parts of a zinc finger-type structure (5, 6, 14). These residues coordinate a zinc ion and are therefore expected not to be available to form disulfide bridges in the native structure of IN. Indeed, substitution of cysteine 40 or 43 by alanine led to a loss of both integration activity and virion infectivity (7). Mutant proteins C56S, C65S, C130S, and C280S were produced in the baculovirus expression system and were purified in the absence of reducing agent. The oligomeric status of the mutant and wild-type proteins with or without DTT was analyzed by SDS-PAGE (Fig. 2A). The wild-type control (lanes 1 and 5) and C56S and C65S mutations (lanes 6 and 7) formed disulfide-linked dimers. In sharp contrast, the C280S mutation led to a complete absence of covalent oligomers. Thus, cysteine 280 is involved in the disulfide bond formation.
With the C130S mutant, the full-length protein was never obtained. Anti-IN polyclonal antibodies revealed the presence of two proteolysis products with apparent molecular masses of 16 and 18 kDa, although analysis of the IN protein sequence did not reveal a specific protease cleavage site generated by the cysteine-to-serine substitution (data not shown). A similar phenomenon was described for purified virions (23): a mutation at residue 130 caused an instability of the protein and a subsequent loss of the covalent oligomers. This residue is located within the catalytic pocket, and its mutation is known to abolish the enzymatic activity. Presumably, mutation of C130 destructures the catalytic core. This effect may be the cause of the instability of the protein in a eukaryotic expression system.
It is still not clear whether C130 is involved in covalent IN dimerization. C280 is, however, involved in the disulfide bridges, and the plausibility of a C130-C280 disulfide linkage is unclear. According to the recently solved structures of the two- domain IN proteins and the deduced model for the active tetramer, the C130 and C280 residues are too far apart to allow the formation of a disulfide bridge (9, 17, 26). In contrast, an intermolecular disulfide bridge between C280 residues is entirely plausible as models of the IN-DNA nucleoprotein lead to a significant overlap of the C-terminal domains of different protomers (17).
Cysteine 280 is responsible for the disulfide linkage formation in viral particles. IN can form covalent dimers in vitro by bridging C280 residues from independent monomers. We tested whether such disulfide-linked oligomers can be recovered from viral particles. A mutant virus bearing the IN C280S mutation was constructed, and the oligomeric status of its IN was compared to that of the wild-type enzyme. pBRU2 and pBRU2-IN(C280S), carrying BRU2 wild-type and the mutant virus, respectively, were used to transfect HeLa cells. Viral particles were recovered from the culture supernatant 72 h later. Viral production was measured as HIV-1 p24 antigen release. No quantitative differences were detected between wild-type and mutant virus, suggesting that the IN(C280S) mutation had no major impact on virus production and release (data not shown). A quantity of virus corresponding to 75 ng of p24 protein was lysed in the absence of reducing agent and analyzed by Western blotting using polyclonal anti-IN antibodies. To test for disulfide bridges, the viral extracts were heated either in the presence or in the absence of ß-mercaptoethanol (Fig. 2B). In the presence of the reducing agent, comparable amounts of wild-type and mutant forms of IN were detected with an apparent molecular mass corresponding to that of the monomer. Thus, the C280S mutant IN was correctly encapsidated in the viral particles (compare lanes 1 and 3). Stable dimers of wild-type IN were observed in the absence of the reducing agent, demonstrating the presence of disulfide-bridged IN dimers in viral particles. However, no covalent dimers were observed with the C280S IN virus mutant (lanes 3 and 4) even in the absence of the reducing agent. This strongly suggests that cysteine 280 is the only residue involved in the formation of disulfide bridges in viral particles as observed in vitro.
The C280S mutation does not affect IN activity in vitro. We investigated the effects of the cysteine mutation on the catalytic activity of IN. Both 3' processing and the subsequent strand transfer activity of the IN cysteine mutants were assayed and compared to the activity of the wild-type protein. Assays were carried out in Mn2+ - or Mg2+-containing buffer because previous reports suggested that the oligomeric states involved in Mn2+- and Mg2+-dependent activities might be different (22). In the presence of a reducing agent, all the proteins were active under these conditions (Fig. 3A). However, the 3'-processing and strand transfer activity of the IN(C280S) mutant was slightly higher than that of the wild-type protein (compare lanes 2 and 5 and lanes 7 and 10). In contrast, the activities of C56S and C65S mutated proteins were not distinguishable from that of the wild-type protein. To avoid possibility that an effect of a cysteine mutation might be masked in an assay monitoring IN activity on short oligonucleotides, the experiment was repeated with the 492-bp miniviral substrate in the presence of heterologous plasmid DNA target. No further effect was observed (data not shown).
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FIG. 3. Influence of the disulfide bridges on 3'-processing activity. (A) Effect of the cysteine-to-serine mutations on in vitro IN activity. Assays were performed with 3.2 nM32P-labeled U5 substrate and 100 nM purified IN incubated for 1 h at 37°C in 20 mM HEPES buffer (pH 6.8) containing 10 mM MgCl2 (lanes 1 to 5) or 10 mM MnCl2 (lanes 6 to 10). The reaction products were resolved on an 18% acrylamide denaturing gel. Wt, wild type. (B) Influence of disruption of the disulfide bridges on wild-type IN 3'-processing activity. In vitro assays were performed with 3.2 nM32P-labeled U5 substrate and 100 nM purified IN incubated for 1 h at 37°C in 20 mM HEPES buffer (pH 6.8) containing 10 mM MgCl2 and one of a series of concentrations of reduced glutathione (GSH). The oligomeric status of wild-type IN was quantified by SDS-PAGE using densitometry analysis. The percent activity was standardized to the activity of IN(C280S) in the absence of glutathione. Striped bars indicate the percentage of monomer as assessed by denaturing gel electrophoresis; gray bars indicate the 3'-processing activity of wild-type IN; black bars indicate the 3'-processing activity of IN(C280S).
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C280S mutation does not affect IN oligomerization. In a previous study, we showed that the ability of IN to use Mg2+ efficiently as a cofactor was related to its oligomerization properties in solution (19). Here we show that the disruption of the disulfide linkage increased the IN activity. We investigated the effect of the presence of a reducing agent (DTT) on oligomerization in solution by fluorescence anisotropy decay measurements. One major cause of light depolarization is the size of the fluorescent macromolecule. Accordingly, small fluorophores, characterized by fast tumbling, give rise to a fast anisotropy decay whereas large fluorophores, with slower rotational motions, yield a slower anisotropy decay. The effect of DTT addition on the IN depolarization curves is shown in Fig. 4. The anisotropy decay of the protein was significantly slower in the presence of 5 mM DTT. This indicates that the noncovalent monomeric units observed on denaturing gels have a propensity to reorganize in solution into a multimeric protein which is not cross-linked by disulfide bridges. Maximum-entropy method analysis of these decays was performed (data not shown). In the absence of DTT, IN is characterized by a broad distribution of long correlation times centered at 30 ns, suggesting a heterogenous solution. Addition of DTT gave rise to a well-defined long correlation time, centered at about 75 ns, consistent with a homogenous tetrameric form (10). For the C280S mutant, no significant differences were observed between reducing and nonreducing conditions (data not shown). Moreover, the decays lines obtained with the mutant and the those obtained with the wild type under reducing conditions were superimposable. These results indicate that the mutant and wild-type proteins were characterized by comparable oligomeric states in the presence of DTT. We conclude that although no functional difference was observed in vitro between the wild-type and C280S mutant IN proteins, transitory formation of covalent dimers is possible as disulfide bridges may transiently form during an early step of the enzyme production.
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FIG. 4. Study of the oligomerization status of IN by fluorescence anisotropy decay. The fluorescence of 200 nM IN was monitored. The lifetime distribution was 0.195 ns (14%), 0.45 ns (25%), 1.3 ns (21%), 2.7 ns (27%), and 5.1 ns (13%). The figure shows the line fits resulting from maximum-entropy method analysis of the anisotropy decays (grey line, no DTT; black line, 5 mM DTT). The inset shows the corresponding experimental decays.
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Covalent dimers are not required for HIV-1 replication either in cycling or in arrested cells. Disulfide bridges are not essential to IN activities in vitro but are present in the viral particle. We investigated whether they are required for the physiological function of IN. The replication of the virus bearing the IN(C280S) mutation was first monitored in two cellular models of dividing cells. Both CEM4fx cells and phytohemagglutinin (PHA)-stimulated PBLs were infected de novo with either the wild-type or mutant virus, obtained by transfection of HeLa. p24 production was monitored for 9 days (Fig. 5A and B). For both viruses, viral production was detectable 48 h postinfection and peaked on day 6. The mutation had no impact on replication efficiency in CEM4Fx (Fig. 5A). Thus, the absence of disulfide linkage of IN oligomers did not impair the replication cycle in dividing cells. Viral replication was also comparable in the activated lymphocytes (Fig. 5B), although on day 5 the curve describing the mutant virus production showed a slight inflexion, giving rise to a final deviation from the wild-type curve of approximately 20%. This difference remained limited, demonstrating that destabilization of the covalent dimers did not prevent viral replication. PHA stimulation of PBLs is usually 80 to 90% effective but leaves a subpopulation of the cells in a noncycling state. Therefore, this experiment does not show that there is a true difference in the viral replication in suboptimally stimulated lymphocytes.
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FIG. 5. Comparison of BRU2 and BRU2-IN(C280S) virus infection in dividing and nondividing cells. (A) Replication of wild-type and IN(C280S) virus in CEM4fx cells. (B) Replication of wild-type and IN(C280S) virus in PHA-stimulated PBLs. Equivalent amounts of wild-type (BRU2) () or mutant [BRU2-IN(C280S)] ( ) viruses were used to infect CEM4fx cells (2.5 ng of p24/7,500 cells) (left) or PBLs (0.5 ng of p24/7,500 cells) (right). Virus production was monitored as the accumulation of p24 antigen in culture supernatants. p24 antigen production was assayed with the HIV p24 ELISA kit (NEN). (C and D) Cell cycle distribution of P4 cells before (C) and after (D) aphidicolin treatment (16 h). (E) Early steps of replication of wild-type and IN(C280S) virus in either P4 cells or G1-arrested aphidicolin-treated P4 cells. The ß-galactosidase (ß-gal) activity of infected P4 cells was monitored after lysis and incubation with chlorophenolred-ß-D-galactopyranoside (CPRG). The reaction product was quantified using a multiscan photometer at 570 nm. BRU2 ( ) and BRU2-IN(C280S) ( ) infection in dividing P4 cells and BRU2 ( ) and BRU2-IN(C280S) ( ) infection in nondividing aphidicolin-treated P4 cells are shown. Various quantities of virus, measured as p24 contents, were used to infect dividing or nondividing P4 cells (5 x 104 cells) for 48 h.
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In conclusion, both the recombinant IN produced in insect cells and the physiological enzyme recovered from viral particles can form disulfide-linked covalent dimers. Residue C280 is the only residue responsible for the formation of the disulfide bridges. Our findings conflict with those of a previous study suggesting that covalent multimerization of IN may be important for viral replication (23). Nevertheless, we observed a small but detectable difference between the replication efficiencies of the mutant and wild-type viruses in PBLs. This may reflect a functional role in a physiological context that remains to be identified.
This research was supported by grants from the Centre National pour la Recherche Scientifique (CNRS), l'Agence Nationale de Recherche contre le SIDA (ANRS), and Ensemble contre le Sida (ECS). J.B. gratefully acknowledges a fellowship from ANRS.
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