Human immunodeficiency virus type 1 (HIV-1) encodes protease (PR), reverse transcriptase (RT), and integrase (IN) as parts of a large Gag-Pol precursor polyprotein (Pr160
Gag-Pol). Pr160
Gag-Pol plays an important role in virion assembly and is essential for the formation of infectious virions (for a review, see reference
11). Mutagenesis of the C-terminal region of Pr160
Gag-Pol (RT and IN domains) has been associated with defects in virion assembly, release, maturation, and protein composition (
2,
4,
7,
8,
26,
31). Consequently, these defective viruses may appear to be impaired in early steps of the virus life cycle, such as uncoating and viral DNA synthesis.
Molecular genetic analysis of IN has revealed pleiotropic effects of mutations among different retroviruses. Mutation of nonconserved amino acids within the IN gene of Ty3 (a retrovirus-like element of
Saccharomyces cerevisiae) affects multiple stages of the retrotransposition life cycle, including RT and IN expression, 3′-end DNA processing, and nuclear entry (
23). These mutations also appear to reduce the level of replicated DNA despite normal levels of exogenous RT activity and capsid maturation (
23). Certain point mutations or linker insertion mutations in the Moloney murine leukemia virus (MLV) IN domain impair virion production and proteolytic processing of Gag and Pol (
27-
29). Similarly, certain HIV-1 IN mutations can cause defects in virion assembly, production, maturation, and nuclear import of the preintegration complex (
2-
5,
7,
26,
31). Mutations in the HIV-1 IN coding sequence have been shown to impair viral DNA synthesis in infected cells. Mutations that inhibit translation of the entire IN protein or a small portion (22 amino acids) of its carboxy terminus reduce the amount of early viral DNA products detected by PCR, and viruses containing either point mutations in the N-terminal zinc finger or the central domain (F185) exhibit a similar phenotype (
7,
8,
18,
20,
37).
Because of the pleiotropic effects of
IN mutations,
trans-complementation approaches have been exploited to help analyze the role of the mature IN protein in early steps of the virus life cycle. By expressing viral protein R (Vpr)-IN fusion protein (Vpr-IN) in
trans with HIV-1, IN can be assembled into progeny virions via the interaction of Vpr with Gag and then liberated by the viral protease (
38,
39). Studies with IN mutant viruses that exhibit a defect in DNA synthesis demonstrated efficient complementation by the
trans-IN protein (
37).
trans-Complementation has also been used successfully to study the early IN function of Ty3 and MLV. The DNA synthesis defect of an IN mutant MLV was complemented by expressing MA-CA-IN fusion protein in
trans, and the expression of a CA-RT-IN fusion protein complemented transposition and increased the amount of cDNA of some Ty3 IN mutants (
16,
22). Similar to HIV-1,
trans-complementation of Ty3 and MLV DNA synthesis did not require catalytic activity of the
trans-IN protein.
The HIV-2 (strain ST) IN shows 58% identity with the HIV-1 (strain SG3) IN at the amino acid level. Complementation analysis with a heterologous (HIV-2)
trans-IN protein (Vpr-IN
2) was used to probe for virus- and integrase-specific interactions required for efficient cDNA synthesis. By complementing an IN mutant of HIV-1 that produced a wild-type level of cDNA but was defective in integration, the
trans-IN
2 protein was shown to integrate (55% of wild-type activity) HIV-1 provirus into the DNA of infected cells (
19). This is consistent with in vitro studies that demonstrated that HIV-2 IN supports 3′-end processing and strand transfer of an oligonucleotide substrate that mimics the end of the HIV-1 viral DNA molecule (
34). However, the heterologous
trans-IN
2 protein did not efficiently complement viral DNA synthesis, suggesting that this function requires virus type-specific interactions between the integrase protein and other components of the reverse transcription complex (
19,
37).
To further analyze the effect of IN on the initiation of HIV-1 DNA synthesis, we took advantage of a chimeric HIV-1 virus (SG3
IN2) in which the HIV-2
IN coding region (IN
2) was inserted in place of the cognate
IN. This chimeric virus exhibits a severe defect in infectivity and DNA synthesis (
19). In this report, we describe the emergence, isolation, and characterization of culture-selected chimeric viruses. Genetic analysis demonstrated that the selected viruses contained mutations in various regions of the viral genome, including the RT and IN
2 coding sequences. By expressing the mutated IN
2 as a Vpr-IN
2 fusion protein in
trans with HIV-1 integrase-defective virus, we demonstrated that mutations in IN (Q96H, V204I, and K127E) significantly increased viral DNA synthesis and were principally responsible for the improved fitness of the chimeric virus. The results of this study implicate specific regions on the IN proteins that may play a role in augmenting HIV-1 DNA synthesis.
DISCUSSION
In this study, we use a chimeric virus that was severely defective in DNA synthesis to select viruses with improved replication fitness. Analysis of the most replication-fit virus demonstrated that improved fitness was largely due to compensatory amino acid changes selected in IN2. These mutations were shown to increase virus fitness largely by augmenting the initiation of reverse transcription. Importantly, our trans-complementation analysis indicate that the IN mutations enhanced DNA synthesis by an effect on the mature IN2 protein itself on an early step in the virus life cycle. Considering the high degree of structural homology between the HIV-1 and HIV-2 IN proteins, the mutations selected in IN2 may implicate regions on the HIV-1 IN protein that are important for the initiation of DNA synthesis.
Our analysis was focused on viruses that were derived after 65 and 131 days of cell-free passage. The CF-131 virus was studied because it was the most infectious, while the CF-65 virus was significantly less infectious and represented a biological and temporal intermediate form of chimeric virus. To facilitate molecular genetic analysis of these viruses, a 5.3-kb DNA fragment comprising most of the 5′ end of the viral genome was cloned into the naturally existing BssHII and SalI restriction sites of the pNL4-3 clone. The most infectious clones derived at each time point exhibited a level of infectivity similar to that of the respective parental virus. This result indicated that the 5′ DNA segment of the chimeric virus was largely responsible for the improved viral fitness.
Sequence analysis of four clones derived from the CF-65 virus identified amino acid mutations that were mostly restricted to RT and IN
2. Mutations in RT were heterogeneous, while each clone contained the V204I IN mutation, suggesting that it had become fixed in the cell-free chimeric virus population. These results may suggest that the selection of mutations in RT and/or IN enabled cell-free transmission and productive infection of the CF-65 chimeric virus. This idea was in part validated when these two regions were analyzed in
cis and found to improve infectivity (Fig.
4). In the evolution of the CF-131 virus, the Q96H, K127E, and V204I IN mutations were selected and appeared to be principally responsible for the increased level of infectivity and DNA synthesis. Interestingly, with the exception of V179I, most of the other CF-65 RT mutations were lost during the evolution of the CF-131 virus. Analysis of the CF-131 RT in
cis indicated that the V179I mutation had little or no effect on virus infectivity by itself but together with the three IN mutations (Q96H, K127E, and V204I) augmented infectivity to a level close to that of the 3A17 clone (Fig.
4). While the RT and IN mutations appear to account for most of the improvement in virus infectivity, mutations detected in other regions of the virus genome do warrant further study.
By expressing and packaging IN in
trans, it is possible to discriminate between the effect of IN mutations on early versus late events of the virus life cycle (
38). Therefore, several studies of IN function have exploited
trans-expression approaches to help elucidate its role in augmenting viral DNA synthesis (
22,
30,
33,
37,
40). In this study, the 3A17 virus contained multiple mutations that could possibly affect different viral proteins and different steps of the virus life cycle. By expressing the IN mutations found in CF-65 and CF-131 viruses in
trans, we were able to analyze how changes specific to the IN protein affected virus infectivity and DNA synthesis without introducing these mutations into the Gag-Pol (IN domain) precursor protein.
Consistent with our analysis in
cis, the
trans-IN
Q96H, K127E, V204I mutant rescued virus infectivity by approximately 58% compared with the homologous
trans-IN
1 (Fig.
5A) and complemented strong-stop DNA synthesis at least as efficiently as the homologous
trans-IN
1 (Fig.
5B). Analysis of the different IN mutations revealed a strong correlation between their effects on infectivity and on DNA synthesis. One exception was observed when comparing IN
KQ96H, K127E with IN
Q96H, K127E, V204I. While
trans-IN
Q96H, K127E, V204I reproducibly rescued DNA synthesis better than IN
KQ96H, K127E, the opposite was true for virus infectivity (compare Fig.
5A and
5B). The V204I mutation was selected early and remained fixed during the evolution of the chimeric virus. Since the presence of this mutation in
cis appeared to increase relative infectivity greater than when provided in
trans, this mutation may correct a late-stage event. The IN
Q96H mutation reduced DNA synthesis and integration, but in combination with IN
K127E, both were increased. This could suggest that the Q96H and K127E mutations are synergistic and that the IN
2 surface region containing these two residues may be important for augmenting DNA synthesis.
To further understand the effect of mutations on IN
2, we modeled its secondary structure. The catalytic domain of HIV-2
ST IN (residues 55 to 208) shows 90% sequence identity (98% homology) with IN from simian immunodeficiency virus (IN
SIV). We used the crystal structure of the catalytic domain of IN from SIV (PDB/1C6V) as the starting model in the program Swiss-Model, and the resultant coordinates were subjected to Procheck analysis (
17) to assess the final quality of the model. All three mutations in IN
2 were present on a surface that is opposite that of the catalytic triad (shaded red on the ribbon diagram in Fig.
7A). Two mutations, Q96H and K127E, were present on adjacent helices and separated by a distance of 12.56 Å (between Cα's). Furthermore, residue K127E brings about a contrast in the net local charge, from positive to negative, while the Q96H mutation marginally changes the net potential. Interestingly, the V204I mutation converts this residue back to the HIV-1 and HIV-2 consensus, and the surface in this region closely resembles that of HIV-1 IN.
Our analysis of the CF-65 virus indicated that changes in RT augmented viral DNA synthesis (Fig.
5). Sequence analysis of the CF-65 virus revealed that three of the four clones had mutations (K102R, V179I, D237N, and D320N) that clustered around the nonnucleoside RT inhibitor (NNRTI) binding pocket on RT (Fig.
7B). Except for V179I, a conserved hydrophobic mutation which is a part of the NNRTI binding pocket, the K102R, D237N, and D320N mutations are present on the outer surface of this pocket in very close proximity and invoke a net change in the potential on the surface. Our data indicate that these represent compensatory mutations that improve the infectivity of the CF-65 virus (Fig.
4). Their presence on the outer surface of the NNRTI binding site could imply a role for this region in triggering DNA synthesis. However, there is no clear evidence at the moment to corroborate this argument, and it certainly warrants further study.
Our data clearly show that changes in IN and RT affect DNA synthesis. In other studies with recombinant proteins in pulldown assays, IN and RT as well as MLV RT and IN have been shown to interact physically in vitro (
12,
13,
32,
37). A recent study demonstrated that monoclonal antibodies generated against the minimal DNA binding domain in the C terminus of IN block the interaction of recombinant IN and RT (
13). Biochemical analysis demonstrating that HIV-1 RT and IN inhibit each other's function (
24,
32) perhaps suggests interaction between these proteins during early stages of the virus life cycle. In our study, it was notable that many of the CF-65 clones contained RT mutations proximal to the hydrophobic pocket, conferring a slight change in charge. Except for V179I, these mutations were lost while additional mutations were selected in IN
2, ultimately leading to a fitter virus. These results give a snapshot of how the RT and IN
2 genes appeared to coevolve to ultimately generate a virus with a greater capacity to synthesize viral DNA in infected cells.
Taken together, our findings indicate an important biological role for IN in the initiation of reverse transcription. It is consistent with our model that specific interactions between IN and other components that comprise the initiation complex are required to prevent premature initiation, thus ensuring association of IN with the nuclear preintegration complex and integration of the provirus upon the completion of reverse transcription.