Recovery of fitness of a live attenuated simian immunodeficiency virus through compensation in both the coding and non-coding regions of the viral genome
© Whitney and Wainberg; licensee BioMed Central Ltd. 2007
Received: 07 February 2007
Accepted: 03 July 2007
Published: 03 July 2007
We have analyzed a SIV deletion mutant that was compromised both in viral replication and RNA packaging. Serial passage of this variant in two different T-cell lines resulted in compensatory reversion and the generation of independent groups of point mutations within each cell line. Within each group, single point mutations were shown to contribute to increased viral infectivity and the rescue of wild-type replication kinetics. The complete recovery of viral fitness ultimately correlated with the restoration of viral RNA packaging. Consistent with the latter finding was the rescue of Pr55 Gag processing, also restoring proper virus core morphology in mature virions. These seemingly independently arising groups of compensatory mutations were functionally interchangeable in regard to the recovery of wild type replication in rhesus PBMCs. These findings indicate that viral reversion that overcomes a genetic bottleneck is not limited to a single pathway, and illustrates the remarkable adaptability of lentiviruses.
The packaging of full-length viral genomic RNA (vRNA) into primate lentiviruses is regulated by a multipartite cis-acting signal located within the 5' untranslated region (UTR) or RNA-leader. In the leader of human immunodeficiency virus type-1 (HIV-1), the packaging signal or Psi (Ψ) is distributed across multiple RNA domains that include stem loop-1 (SL1), SL3 and SL4 [1–3]. There is also evidence of vRNA packaging elements in other regions, including those upstream of the primer-binding site (PBS), as well as within downstream gag-coding regions [4, 5].
Comparative packaging studies of simian immunodeficiency virus (SIV) by our group and of human immunodeficiency virus type-2 (HIV-2) by others, have assigned a primary role in packaging to SL1, as compared to all other regions within the SIV and HIV-2 genomes [6–10]. Moreover, SL1 sequences are also important in the formation of 5' linked vRNA duplexes or vRNA dimers [8, 11–13]. RNA-RNA interactions ultimately determine RNA tertiary conformation and have been shown to impact on both the regulation and efficiency of vRNA packaging [14, 15]. The relationships among the packaging events of different lentiviruses have been extensively studied .
The foregoing implies the presence of multiple RNA-binding domains within Pr55 Gag. In the context of Pr55 Gag an important trans-role has been ascribed to the viral nucleocapsid (NC) protein [17, 18], although several studies have indicated that a functional separation of domains within NC is present [17, 19]. Other protein domains within Gag have also been shown to be necessary for vRNA packaging and dimerization, whereas the p2 region has been shown to contribute to vRNA packaging specificity [20, 21].
Studies on the reversion of SL1 deleted virus in HIV-1 showed that compensatory point mutations in four distant Gag proteins, i.e. nucleocapsid (NC-T24I), matrix (MA-V35I), capsid (CA-T24I) and the p2-spacer (p2-T21I) were all involved in restoration of viral growth . Griffin et al have shown that there is a preferential use of co-translation to impart packaging specificity for vRNA in HIV-2 . A similar process is thought to occur in SIV, particularly in light of evidence that the 3' regions of the leader possess an internal ribosome entry site (IRES) function .
Although Pr55Gag alone has been shown to be sufficient for particle production, numerous host and viral proteins are required for optimal viral assembly and budding . Indeed, an appropriate conformation of packaged RNA is critical, since mutations in viral RNA can severely impact virus production and viability . The late phase of lentiviral replication requires the assembly of virion components at the cellular periphery, at which a series of interrelated vRNA-protein interactions are required to occur in a coordinated fashion; this positions vRNA in precise relation to Pr55Gag during protease-mediated cleavages that take place during assembly and at post-budding stages .
Previous work from our group described a mutant deleted of 21 nucleotides within the 5' proximal stem of SL1 of the infectious molecular clone of SIVmac239 (Δnt +398 to +418, termed-SD2) that resulted in a significant delay in viral replication and reduced vRNA packaging. The serial passage of this mutant virus in the CEMx174-T/B-hybrid cell line or in C8166-T cells over protracted periods resulted in the recovery of virus replication . Our previous report showed that the original SD2 deletion had been retained, but that each cell line specific isolate harboured three additional compensatory point mutations.
The present study was designed to elucidate mechanisms whereby various compensatory mutations can restore viral replicative fitness, and the role of different cellular environments on the molecular evolution of SIV genomes harboring deletions in leader sequences. We now show that the recovery of Pr55Gag protein processing is commensurate with the return of wild-type levels of packaged vRNA. We also show that some mutations can facilitate partial recovery of RNA dimerization, leading to restored viral core morphology and placement. Thus, compensation may involve different viral gene products, leading to restored infectivity and replicative fitness in primary PBMCs.
The A423G point mutation plays an important role in the restoration of viral RNA packaging
Impact of various coding and non-coding compensatory mutations on SD2 fitness.
Viral DNA of each of the two mutant groups (i.e. generated in either C8166 or CEMx174 cells) were transfected into 293T cells. Mutant viral RNA was extracted from aliquots of the supernatants of these transfections and normalized on the basis of p27-CA. To assess relative packaging efficiency, mutant viral RNAs were used as template in an 18-cycle multiplex RT-PCR reaction run in parallel with multiple dilutions of wild type vRNA as a linear range control, as described previously .
Next, we tested the ability of the two NC mutations to restore vRNA incorporation. Fig 2B shows that the presence in SD2 of either E18G or G31K alone only marginally affected levels of viral RNA packaging. In contrast, the presence of both NC mutations resulted in moderately increased RNA packaging. The addition of the A423G mutation to the construct that contained both NC substitutions completely compensated for the packaging deficit.
The SD2 variant (Δnt +398 to +418, Fig. 1) has also been shown to be devoid of an RNA dimer [6–8]. To determine the impact of multiple compensatory mutations on vRNA dimerization, we analysed purifed vRNA on non-denaturing Northern gels.
Next, we tested the ability of the two NC mutations to rescue vRNA dimerization. Figure 3C shows that the SD2 variant did have slightly increased levels of dimeric RNA in the presence of either E18G or G31K. In contrast, the presence of both NC mutations resulted in a moderate increase in levels of dimeric RNA. The addition of the A423G and E18G mutations to the SD2 parental strain also yielded an increase in RNA dimer levels. Finally, the addition of G31K or of both NC substitutions to the SD2-A423G variant increased levels of both packaged RNA monomer and dimer.
To shed further light on the mechanisms involved, we performed a thermodynamic RNA structural analysis of these mutants by using M-Fold software . RNA secondary structure analysis suggests that the A423G point mutation, that is located in the DIS-SL loop, cannot restore native DIS-SL structure. However, our analysis indicated that the A423G mutation altered the size of the DIS-loop through nucleotide reorganization and loss of SL2 structure (not shown). Hence, the A423G point mutation plays an important role in the compensation of the SD2 deletion, but a full correction of packaging requires the presence of three mutations.
The G49K point mutation within p6 or, alternatively, the E18G and G31K mutations within NC can restore Pr55Gag processing in viruses that harbour the SD2 deletion
The results of Fig. 4B show that either the E18G or G31K substitution in NC was independently able to facilitate complete Pr55Gag processing in the SD2 virus. In the presence of the A423G mutation, however, both NC mutations i.e., SD2-A423G, E18G, G31K, were required to restore processing of both the MA-CA (p41) and CA-NC (p39) intermediate processing products, leading to a wild type processing phenotype.
Thus, the A423G point mutation acts to rescue the deficit in viral RNA packaging of the SD2 deletion, while the G49K mutation in p6 or the E18G and G31K substitutions in NC contribute to the restoration of Gag processing.
Both sets of compensatory mutations are functionally interchangeable in recovery of viral replication and infectivity
The role of these various compensatory mutations in viral replicative fitness was next assessed on the basis of viral infectiousness in CEMx174 cells. For this purpose, relative p27-CA concentrations in viral supernatants at the peak of viral replication (as determined by RT assay and observed cytopathicity in culture) were used to calculate TCID50 per ng p27-CA antigen (Fig. 5C). The results show that the SD2 mutant was severely compromised, whereas each compensatory mutation was independently capable of restoring some degree of viral infectiousness, with the largest increase attributable to A423G. However, recovery to near wild-type replication levels required a full complement of either of the two groups of compensatory mutations. The mutations identified in the C8166 cell line restored infectiousness equally well when assayed in the CEMx174 line and vice versa (not shown). Thus, both sets of compensatory mutations seem to be functionally interchangeable in regard to restoration of viral replication, independent of the cell line in which they were first selected.
Forced evolution results in restoration of proper viral core ultra-structure
Both recombinant clones (i.e. SD2-A423G-E18G-G31K and SD2-A423G-K197R-G49K) were also transfected in parallel, and yielded comparable levels of particle production as wild type, as measured by p27-CA levels in culture supernatants (not shown). The results of the EM experiments showed restoration of proper core morphology, and levels of immature virus were comparable to the wild type (Fig. 6).
Here, we describe an SIV deletion mutant that was passaged in two different T-cell lines and that employed two different pathways to attain reversion. Retroviruses display genomic plasticity, and sequence diversification in both HIV-1 and SIV can in some cases augment viral replication and pathogenesis [29–31]. The fitness of an RNA virus population may be viewed as a continuum of genomes of varying fitness. It is not surprising that these viruses may be able to employ diverse routes to reach higher fitness levels. However, such transitions may be delimited by the tolerance of a particular gene for non-synonomous mutation versus the maintenance of a native function. In the case of mutations that compensate for deletion mutagenesis, a debilitated variant should need to pass through a deterministic bottleneck to initiate a new quasispecies distribution. Therefore, compensation should be governed by selection for optimal viral fitness and not by stochastic drift .
Our findings indicate that reversion is not limited to a single trajectory. Compensatory mutations in both the untranslated leader and the gag-coding region emerged during long-term passage in different T-cell lines, and these mutations were required for full restoration of viral replication. Interestingly, the A423G substitution, located within the DIS, was shown to be active in restoring efficient levels of viral RNA packaging, while mutations in either the nucleocapsid, G31K, E18G, or within the p6 protein of Gag, G49K, were essential for the proper processing of Gag precursors. In each instance, the presence of three point mutations was functionally synergistic in regard to rescue of both viral RNA packaging and Gag processing. Moreover, the observed changes in regard to impaired Gag processing could be corrected by either the E18G, G31K or G49K mutations. We also showed that RNA dimerization could be partially recovered due to compensatory mutations in NC. Several studies have shown the interplay that exists between viral RNA and viral proteins that are involved in regulation of core structure, proteolytic processing, and maturation of RNA dimers [34, 35]. Interestingly, SD2 mutants harboring A423G and various combinations of K197R and G49K did co-package a high molecular weight RNA species reminiscent of the "immature" dimer found in protease mutants of MLV .
Numerous studies on HIV-1 have shown that NC is the major protein domain within Gag that recognizes the encapsidation signals present within leader sequences . The NC protein contains two zinc finger motifs that contribute to its specific interactions with viral RNA, including a well-described role in RNA dimer maturation [19, 37]. Deletions within SL1 of HIV-1 were shown to impair viral replication, as well as to cause delayed processing of Gag proteins and decreased levels of packaging of viral RNA . Forced evolution of SL1 deleted virus in HIV-1 showed that compensatory reversion was a result of substitutions in four disparate regions of Gag, i.e. NC (T24I), MA (V35I), CA (T24I) and p2 (T21I) . These substitutions all involve hydrophobic amino acids. In contrast, we have shown that the deletions in leader sequences of SIVmac239 can be rescued by compensatory point mutations elsewhere within the DIS and Gag. The present work shows that restoration of SIV replication involved two distinct sets of mutations, located in both the DIS loop (A423G) and within different Gag proteins, i.e. NC (E18G and G31K) or CA (K197R) and p6 (E49K); these amino acid changes, with the exception of K197R, result in a net increase in the number of positively charged residues within Gag.
The finding that mutations within NC can rescue these deficits further confirms the role of this protein in interactions between Gag and RNA leader sequences of SIV, which have been less intensively studied than for HIV. The debilitated SD2 virus may be able to correct the deficit caused by the deletion within the DIS stem by altering both the leader sequence, as well as by reconfiguring Gag proteins, presumably to facilitate both viral RNA-RNA and RNA-protein interaction [39, 40].
Our data also show that p6 plays an important role in the incorporation of viral proteins into virions and the specific encapsidation of viral RNA . We have also demonstrated that a substitution within p6 resulted in comparable levels of compensation as did mutations within NC, i.e. E18G or G31K, in restoration of Gag processing. This suggests that p6 may also be important at core positioning and condensation during viral budding. The multimerization of Pr55 Gag has been shown to occur on an RNA scaffold, and encapsidation of viral RNA likely requires that leader RNA sequences exist within the constraints of proper tertiary structure, which are highly conserved in both HIV-1 and SIV [40, 42–44]. Deletions of leader sequences may alter critical RNA-protein interactions at early stages of viral assembly, thereby altering morphogenesis. As a result, nascent particles may not be able to undergo a "normal" intra-virion transition that condenses the RNA genome and multiple viral proteins to produce a "primed" infectious core .
These observations suggest the importance of functional interactions between Gag-proteins and the RNA-leader in both HIV-1 and SIV, but also imply that important differences may exist between SIV and HIV-1 in regard to such interactions. We have also demonstrated that different cell types can reproducibly select for different sets of compensatory mutations, but that both of these sets are functionally interchangeable in regard to their ability to restore viral replication, regardless of the cell type in which the virus is ultimately grown. Of course, it is conceivable that either the same mutational spectrum or even different ones may have been observed in either of the cell lines tested had additional replication studies been performed.
It is not trivial that the mechanisms of compensation for lentiviruses, grown under conditions of stress as demonstrated here, are apparently not restricted to single pathways. The mechanisms behind viral escape from antibodies, cytotoxic-T lymphocyte pressure and the generation of resistance to antiretroviral drugs are not mutually exclusive. Our results add to what is known about the plasticity and adaptability of lentivirus genomes.
Construction of recombinant proviral SIV clones
A PCR-based mutagenesis method was applied together with conventional cloning techniques using the full-length infectious clone of SIV, termed SIVmac239 wild type as a template, to generate all the mutants described . All nucleotide designations are based on published sequences; the transcription initiation site corresponds to position +1 .
Viral RNA packaging analysis by RT-PCR
To study packaging of viral genomic RNA we used methods previously described [6–10]. Briefly, viral RNA was isolated using the QIAamp viral RNA mini kit (QIAGEN) from equivalent amounts of 293T cell-derived viral preparations (normalized by SIV p27-CA antigen). RNA samples were treated with RNase-free DNase I at 37°C for 30 min to eliminate potential plasmid DNA contamination, followed by inactivation by incubation at 75°C for 10 min. The viral RNA samples were quantified using the Titan One Tube RT-PCR system (Boehringer Mannheim, Montreal, Quebec, Canada). The primers sg1 and sg2 were used to amplify a 114-bp fragment within the MA coding region of gag representing full-length viral RNA. The primer sg2 was radioactively labeled with δ-P32-ATP in order to visualize PCR products. Equivalent RNA samples, based on p27 antigen levels, were used as templates in an 18-cycle RT-PCR. The products were fractionated on 5% polyacrylamide gels and exposed to X-ray film. Relative amounts of products were quantified by molecular imaging (BIO-RAD Imaging). RNA encapsidation was determined on the basis of four different reactions, and calculated with wild type virus levels arbitrarily set at 1.0.
Non-denaturing Northern analysis
Culture fluids from transfected 293T cells were collected and clarified using a Beckman GS-6R bench centrifuge at 3,000 rpm for 30 min at 4°C. Viral particles were further purified through a 20% sucrose cushion at 40,000 rpm for 1 hour at 4°C using a SW41 rotor in a Beckman L8-M ultracentrifuge. Viral pellets were first dissolved in Tris-EDTA (TE) buffer, then in lysis buffer containing proteinase K (100 μg/ml) and yeast tRNA (100 μg/ml). Samples were incubated for 20 min at 37°C, in the presence of 50U of DNAse I, followed by two extractions, first in phenol: chloroform: isoamyl alcohol, then chloroform. Viral RNA was then precipitated, washed in 70% ethanol and stored at -80°C until required, at which time samples were resuspended in TE buffer at 4°C. RNA was then analysed by non-denaturing electrophoresis on 0.9% agarose gels in 1× Tris-Borate-EDTA (TBE) running buffer for 4 hrs at 4°C. Products were subsequently denatured in 50 mM NaOH and equilibrated in 200 mM Na-acetate. Following electrophoresis, RNA was transferred to Hybond-N nylon membranes by capillary blotting using a 20× concentration of SSPE buffer. Membranes were baked for 2 hrs at 80°C. Probes were prepared by digestion and purification of the NdeI-BstE III fragment excised from the SIVmac239 plasmid. These were recovered by gel purification and labelled with δ-P32-ATP by nick-translation following standard protocols (Roche, Indianapolis, IN, USA). The denaturing Northern analysis of cellular RNA was also conducted in parallel. RNA extraction was carried out in similar fashion to that described for slot blotting above. Cellular RNA from lysates was normalized on the basis of p27-CA antigen present in cellular lysates. Total cellular RNA preparations, i.e. equivalent volumes of RNA, were also run on 1% ethidium bromide (EtBr) stained gels as internal controls for total RNA and 28S and 18S ribosomal RNAs. Probes were prepared as described above. Probes were labelled by nick-translation following standard manufacturer's protocols (Roche, Indianapolis, IN, USA) and used in standard hybridization reactions.
Western analysis of viral protein
At 48 hrs post-transfection, virus-containing supernatants recovered from transfected 293T cells were collected and clarified at 3000 rpm for 30 min, at 4°C in a GS-6R Beckman centrifuge. Virus was further purified by pelleting through a 20% sucrose cushion by ultracentrifugation at 35000 rpm in a Beckman ultracentrifuge for 1 hr at 4°C. Cells were washed 2× in cold PBS and lysed by the addition of buffer containing 1% Nonidet P-40, 50 mM Tris-CL (pH 7.4), 150 mM NaCl, 0.02% sodium azide, and a cocktail of protease inhibitors (Roche, Laval, Quebec, Canada). Virus was normalized on the basis of p27-CA protein present in supernatants or cell lysates. Both pelleted virus and cellular lysates were subject to Western blotting with monoclonal antibodies directed at SIV p27-CA antigens (Fitzgerald industries, MA, USA) following standard protocols .
Cell culture and preparation of virus stocks
293T cells were maintained in DMEM medium supplemented with 10% heat-inactivated fetal bovine serum, penicillin, streptomycin and glutamine. CEMx174 or C8166 cells were maintained in RPMI-1640 medium supplemented with 10% heat-inactivated fetal bovine serum and antibiotics. All media and sera were purchased from Gibco inc. (Burlington, Ontario, Canada).
Monkey peripheral blood mononuclear cells (PBMCs) were isolated from the blood of healthy rhesus macaques (Macaca mulatta) housed at L.A.B. Pre-Clinical Research International Inc., (Montreal, Quebec). All primates were housed in accordance with accredited laboratory care standards. All donor macaques were tested serologically and were negative for simian type-D retrovirus-1 (SRV-1), simian T-cell lymphotrophic virus type 1(STLV-1), and simian foamy virus (SFV-1) at the initiation of the study.
PBMCs were purified on Ficoll cushions, washed in supplemented RPMI-1640 media, and purified lymphocytes were then phytohemagglutinin (PHA)-stimulated for 3 days, then maintained in supplemented RPMI-1640 medium containing 10% heat-inactivated fetal bovine serum and 20 u/ml IL-2 at 37°C with 5% CO2 overlay. All recombinant viral constructs were purified using a maxi-plasmid purification kit (Qiagen inc. Mississauga, Ontario, Canada). For the production of infectious viral stock, 293T cells were transfected using the above constructs together with Lipofectamine-Plus reagent (Gibco, Burlington, Ontario, Canada). Virus-containing culture supernatants were harvested at 48 hr post-transfection and clarified by centrifugation for 30 min at 4°C at 3,000 rpm in a Beckman GS-6R centrifuge. Viral stocks were passed through a 0.2 μm filter and stored in 1 ml aliquots at -80°C. All wild type and mutant stocks were titered on the basis of p27-CA antigen in culture supernatants using a Coulter SIV core antigen ELISA assay (Immunotech inc., Westbrook, ME, U.S.A.).
Virus replication in macaque donor PBMCs
To initiate infection, viral stocks were thawed at room temperature. Then, 100 U of Dnase I in the presence of 10 mm MgCl2 were added at 37°C for 0.5 h to eliminate any potential plasmid DNA contamination, prior to inoculation of cells. Infection of rhesus PBMCs was performed by incubating 4 × 106 PHA-activated cells with wild type or mutant viral stocks containing 10 ng of p27-CA viral equivalent at 37°C for 2 hours. Infected cells were then washed three times with PBS to remove any remaining virus. Finally, cells were resuspended in fresh supplemented RPMI-1640 medium. Cells were maintained in 3 ml of culture medium as described above, and fresh stimulated PBMCs were added to the cultures at weekly intervals. Virus production in culture fluids was monitored by both RT assay and SIV p27 antigen capture assay.
Virus infectivity (TCID50) was determined by infection of CEMx174 cells as described previously. TCID50 results were calculated by the method of Reed and Muench .
Electron microscopic analysis of virion morphology
Viral ultra-structure for the described mutant viruses was examined by transmission electron microscopy. Briefly, COS-7 cells transfected with wild type or mutant SIV constructs were fixed at 48 hours post-tranfection in 2.5% glutaraldehyde/phosphate buffered saline followed by a secondary fixation of lipids in 4% osmium tetroxide. Samples were routinely processed and serially dehydrated. Samples were embedded in Epon under vacuum followed by heat-induced polymerization. Thin-sectioned samples were stained with lead citrate and uranyl acetate and visualized at 80 Kev using a JEOL JEM-2000 FX transmission electron microscope equipped with a Gatan 792 Bioscan wide-angle 1024 × 1024 byte multi-scan CCD camera. At least 100 viral particles were scored for each variant to determine the relative percentage of particles with structural anomalies.
The following reagents were obtained through the AIDS Research and Reference Reagent Program, Division of AIDS, NIAID, NIH: the p239SpSp5' and p239SpE3'plasmids contributed by R. Desrosiers. Research for this study was supported by the Canadian Institutes for Health Research (CIHR). We thank Maureen Olivera for conducting RT assays. We are also grateful to Yonjun Guan for providing the many viral constructs. J. B. W. was supported by both a pre-doctoral and post-doctoral fellowship from The Canadian Institutes for Health Research (CIHR). We are also grateful to Diane and Aldo Bensadoun for support of our work.
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