Modification of a loop sequence between α-helices 6 and 7 of virus capsid (CA) protein in a human immunodeficiency virus type 1 (HIV-1) derivative that has simian immunodeficiency virus (SIVmac239) vifand CA α-helices 4 and 5 loop improves replication in cynomolgus monkey cells
© Kuroishi et al; licensee BioMed Central Ltd. 2009
Received: 12 March 2009
Accepted: 3 August 2009
Published: 3 August 2009
Human immunodeficiency virus type 1 (HIV-1) productively infects only humans and chimpanzees but not cynomolgus or rhesus monkeys while simian immunodeficiency virus isolated from macaque (SIVmac) readily establishes infection in those monkeys. Several HIV-1 and SIVmac chimeric viruses have been constructed in order to develop an animal model for HIV-1 infection. Construction of an HIV-1 derivative which contains sequences of a SIVmac239 loop between α-helices 4 and 5 (L4/5) of capsid protein (CA) and the entire SIVmac239 vif gene was previously reported. Although this chimeric virus could grow in cynomolgus monkey cells, it did so much more slowly than did SIVmac. It was also reported that intrinsic TRIM5α restricts the post-entry step of HIV-1 replication in rhesus and cynomolgus monkey cells, and we previously demonstrated that a single amino acid in a loop between α-helices 6 and 7 (L6/7) of HIV type 2 (HIV-2) CA determines the susceptibility of HIV-2 to cynomolgus monkey TRIM5α.
In the study presented here, we replaced L6/7 of HIV-1 CA in addition to L4/5 and vif with the corresponding segments of SIVmac. The resultant HIV-1 derivatives showed enhanced replication capability in established T cell lines as well as in CD8+ cell-depleted primary peripheral blood mononuclear cells from cynomolgus monkey. Compared with the wild type HIV-1 particles, the viral particles produced from a chimeric HIV-1 genome with those two SIVmac loops were less able to saturate the intrinsic restriction in rhesus monkey cells.
We have succeeded in making the replication of simian-tropic HIV-1 in cynomolgus monkey cells more efficient by introducing into HIV-1 the L6/7 CA loop from SIVmac. It would be of interest to determine whether HIV-1 derivatives with SIVmac CA L4/5 and L6/7 can establish infection of cynomolgus monkeys in vivo.
Human immunodeficiency virus type 1 (HIV-1) productively infects only humans and chimpanzees but not Old World monkeys (OWM) such as cynomolgus (CM) and rhesus (Rh) monkeys . Unlike the simian immunodeficiency virus isolated from macaques (SIVmac), HIV-1 replication is blocked early after viral entry, before the establishment of a provirus in OWM cells [1–3]. This restricted host range of HIV-1 has greatly hampered its use in animal experiments and has caused difficulties for developing prophylactic vaccines and understanding HIV-1 pathogenesis. In order to establish a monkey model of HIV-1/AIDS, various chimeric viral genomes between SIVmac and HIV-1 (SHIV) have been constructed and tested for their replicative capabilities in simian cells. The first SHIV was generated on a genetic background of SIVmac with HIV-1 tat, rev, vpu, and env genes . Although such a SHIV is useful for the analysis of humoral immune responses against the Env protein [5–7], SHIVs containing other HIV-1 structural proteins, especially the Gag-Pol protein, have become highly desirable, since cellular immune response against Gag is generally believed to be important for disease control [8–10].
In recent years, several host factors involved in HIV-1 restriction in OWM cells have been identified. ApoB mRNA editing catalytic subunit (APOBEC) 3 G modifies the minus strand viral DNA during reverse transcription, resulting in an impairment of viral replication [11–13]. This activity could be counteracted with the viral protein Vif [14–17]. Although HIV-1 Vif can potently suppress human APOBEC3G, it is not effective against Rh APOBEC3G, which explains at least partly why HIV-1 replication is restricted in monkey cells. It is well known that Cyclophilin A (CypA) binds directly to the exposed loop between α-helices 4 and 5 (L4/5) of HIV-1 capsid protein (CA), but not to the SIVmac CA. Several studies have found that CypA augments HIV-1 infection in human cells but inhibits its replication in OWM cells [18–20]. A construction of a SHIV with a minimal segment of SIVmac was reported recently by Kamada et al. . This SHIV was designed to evade the restrictions mediated by APOBEC3G and CypA in OWM cells and contains the 7-aa segment corresponding to the L4/5 of CA and the entire vif of SIVmac. The SHIV was found to be able to replicate in primary CD4+ T cells from pig-tailed monkey as well as in the CM HSC-F T cell line. Both in HSC-F and in primary CD4+ T cells, this chimeric virus grew to lower titers than did SIVmac ; and when inoculated into pig-tailed monkeys, this SHIV did not cause CD4+ T cell depletion or any clinical symptoms in the inoculated animals . Another SHIV, stHIV-1 (a virus carrying 202 amino acid residues of SIVmac CA and vif generated by Hatziioannou et al.) could replicate efficiently in Rh cells . However, long-term passaging in Rh cells was necessary to generate an efficiently replicating stHIV-1, and this adapted virus has not yet been fully characterized; so it may be that further modifications of the viral genome are necessary for optimal replication of HIV-1 genomes in OWM cells.
TRIM5α, a member of the tripartite motif (TRIM) family proteins, was identified in 2004 as another intrinsic restriction factor of HIV-1 in OWM cells . Rh and CM TRIM5α were found to restrict HIV-1 but not SIVmac [25, 26]. TRIM5α recognizes the multimerized CA of an incoming virus by its α-isoform specific SPRY domain [27–29] and is believed to be involved in innate immunity to control retroviral infection . Previously, Ylinen et al. mapped one of the determinants of TRIM5α sensitivity in L4/5 of HIV type 2 (HIV-2) CA . In addition, we identified a single amino acid of the surface-exposed loop between α-helices 6 and 7 (L6/7) of HIV-2 CA as a determinant of the susceptibility of HIV-2 to CM TRIM5α . We hypothesized that the L6/7 of HIV-1 CA also determines susceptibility to CM TRIM5α. Here, we investigated whether an additional replacement of L6/7 of HIV-1 CA with that of SIVmac would enhance the replication capability of a SHIV genome in established T cell line HSC-F and in CD8+ cell depleted peripheral blood mononuclear cells (PBMCs) from CMs.
Materials and methods
The HIV-1 derivatives were constructed on a background of infectious molecular clone NL4-3 . NL-ScaVR, a virus containing SIVmac239 L4/5 and the entire vif gene, was constructed according to the procedure described by Kamada et al. . A single amino acid His (H) at the 120th position of NL-ScaVR CA was replaced with Gln (Q) by means of site-directed mutagenesis with the PCR-mediated overlap primer extension method , and the resultant construct was designated NL-ScaVRA1. The L6/7 of CA (HNPPIP) of NL-SVR, NL-ScaVR, or NL-DT5R was also replaced with the corresponding segments of SIVmac239 CA (RQQNPIP) by means of site-directed mutagenesis, and the resultant constructs were designated NL-SVR6/7S, NL-ScaVR6/7S, or NL-DT5R6/7S, respectively. The BssHII-ApaI fragment of NL-ScaVR, NL-SVR6/7S, or NL-ScaVR6/7S, which corresponds to matrix (MA) and CA, was transferred to env deleted NL4-3 (NL-Nhe) to generate the env (-) version of each of the constructs.
Cells and Virus propagation
The 293 T (human kidney), LLC-MK2 (Rh kidney), and TK-ts13 (hamster kidney) adherent cell lines were cultured in Dulbecco's modified Eagle medium supplemented with 10% heat-inactivated FBS. The CD4+ CXCR4+ CM T cell line HSC-F  was maintained in RPMI 1640 medium containing 10% FBS. Virus stocks were prepared by transfection of 293 T cells with HIV-1 NL4-3 derivatives using the calcium phosphate co-precipitation method. Viral titers were measured with the p24 or p27 RetroTek antigen ELISA kit (ZeptoMetrix, Buffalo, NY), and viral reverse transcriptase (RT) was quantified with the Reverse Transcriptase Assay kit (Roche Applied Science, Mannheim Germany).
Green fluorescence protein (GFP) vector
The HIV-1 vector expressing GFP was prepared as described previously [36, 37]. To construct the HIV-1-WT-GFP and HIV-1-L4/5S-GFP vector, we replaced the Eco RI-Apa I fragment corresponding to MA and CA of the pMDLg/p.RRE packaging vector with those fragments from NL4-3 and NL-ScaVR, respectively. The GFP viruses were prepared from 293 T cells in a 15-cm dish by co-transfection with a combination of 24 μg of pMDLg/p.RRE derivatives, 36 μg of CS-CDF-CG-PRE (GFP encoding viral genomic plasmid), 10 μg of pMD.G (vesicular stomatitis virus glycoprotein (VSV-G) expressing plasmid), and 10 μg of pRSV-Rev (Rev expressing plasmid). Forty-eight hours after transfection, the culture supernatants were collected and used for infection.
3 × 105 MT4 or HSC-F cells were infected with 20 ng of p24 of NL4-3, NL-ScaV, NL-ScaVR, NL-ScaVR6/7S, NL-DT5R, or NL-DT5R6/7S. The culture supernatants were collected periodically, and p24 levels were measured with an ELISA kit.
Particle purification and Western blotting
The culture supernatant of 293 T cells transfected with plasmids encoding HIV-1 NL4-3 derivatives was clarified by means of low speed centrifugation. Nine ml of the resultant supernatants were layered onto a 2 ml cushion of 20% sucrose (made in PBS) and centrifuged at 35,000 rpm for 2 h in a Beckman SW41 rotor. After centrifugation, the virion pellets were resuspended in PBS, and p24 antigen concentrations were measured with ELISA. SDS-polyacrylamide gel electrophoresis was applied to 120 ng of p24 of HIV-1 derivatives, and virion-associated proteins were transferred to a PVDF membrane. CA and CypA proteins were visualized with the anti-p24 antibody (Biodesign International, Saco, ME) and the anti-CypA antibody (Affinity BioReagents, Golden, CO), respectively.
HIV-1 derivatives or SIVmac particles were prepared by transfecting each of the env-deleted HIV-1 NL4-3 derivatives or SIVmac plasmids with a plasmid encoding VSV-G into 293 T cells, and culture supernatants were collected two days after transfection. One day before infection, Rh LLC-MK2 and hamster TK-ts13 were plated at a density of 5 × 104 cells per well in a 24-well plate. Prior to GFP virus infection, the cells were pretreated for 2 hours with 200 ng of p24 of each of the HIV-1 or SIVmac particles pseudotyped with VSV-G. Immediately after the pre-treatment, the cells were washed and infected with the HIV-1-WT-GFP or HIV-1-L4/5S-GFP virus. Two hours after infection, the inoculated GFP viruses were washed, and the cells were cultivated in fresh media. Two days after infection, the cells were fixed by formaldehyde, and GFP expressing cells were counted with a flowcytometer. To suppress endogenous TRIM5α activity, the cells were first infected with Sendai (SeV) expressing TRIM5 lacking the SPRY domain at a multiplicity of infection of 10 plaque forming units per cell. Sixteen hours after SeV infection, the cells were treated with 200 ng of p24 of the particles and then infected with the HIV-1-L4/5S-GFP vector as described above.
Preparation of CD8-depleted CM PBMCs and viral infection
CM PBMCs were suspended in RPMI medium 1640 supplemented with 10% (vol/vol) FBS, and the CD8+ cells were removed with a magnetic bead system (Miltenyi Biotec, Auburn, CA) and stimulated for 1 day with 1 μg/ml of PHA-L (Sigma, St. Louis. MO). For prolonged stimulation, CD8-depleted CM PBMCs were first stimulated with 1 μg/ml of PHA-L for 2 days and then with human IL2 100 U/ml for 2 more days. 3 × 105 cells were then inoculated with 200 ng of p24 of NL-DT5R, NL-DT5R6/7S or with 200 ng of p27 of SIVmac239 and incubated at 37°C in a medium containing 100 U/ml of human IL2. The culture supernatants were collected periodically, and the levels of p24 or p27 were measured with an antigen capture assay (Advanced BioScience Laboratories, Kensington, MD)
Construction and characterization of HIV-1 molecular clones containing CA and Vif sequences from SIVmac239
We then introduced SIVmac L6/7 into NL-DT5R, a molecularly cloned virus with two nonsynonymous changes in the env gene gained during long-term passages of NL-ScaVR in HSC-F cells . The resultant virus was designated NL-DT5R6/7S. Although the peak titer of NL-DT5R6/7S was almost the same as that of NL-DT5R, NL-DT5R6/7S could replicate faster in HSC-F than the parental NL-DT5R (Fig. 2C). This finding confirmed that SIVmac L6/7 CA sequence improved the replication in CM cells of HIV-1 derivatives that contained SIVmac L4/5 and vif. The finding suggested that HIV-1 L6/7 and L4/5 CA sequences are important for intrinsic restriction in CM cells.
CypA incorporation into virus particles was not affected by replacement of HIV-1 L6/7 with that of SIVmac
Replacement of both L4/5 and L6/7 of HIV-1 CA with the corresponding loops from SIVmac impaired the CA binding activity of TRIM5α in Rh cells
Endogenous TRIM5α seems to be a likely candidate for the antiviral factor saturated by a high dose of HIV-1 particles (Fig. 4A and 4B). To confirm this, we assessed the ability of WT and mutant HIV-1 particles to saturate the intrinsic restriction factor in the presence or absence of functional TRIM5α. The dominant negative effect of an over-expressed TRIM5 mutant lacking SPRY domain  was used to suppress the function of cell endogenous TRIM5α. As shown in Fig. 4C, the infection of a recombinant SeV expressing TRIM5 without the SPRY domain caused marked enhancement of HIV-1-L4/5S-GFP virus infection without prior particle treatment (crosses vs. asterisks). This indicates that this dominant negative TRIM5 mutant successfully suppressed the restriction activity of endogenous TRIM5α. Treatment with the WT HIV-1 particles also saturated the restriction factors in the cells infected with the empty vector virus (parental Z strain of SeV), while the additional effect of the dominant negative mutant TRIM5α remained unclear (Fig. 4C left, white vs. black squares). These results suggest that the intrinsic factors saturated by the WT particles were mainly endogenous TRIM5α. In contrast to the effect of the WT particle treatment, the effect of the dominant negative TRIM5 mutant on HIV-1 infection was evident when we used particles with SIVmac L4/5 and L6/7 (Fig. 4C, right, white vs. black diamonds, p = 0.007, paired t test). These findings suggest that the diminished capability of particles with SIVmac L4/5 and L6/7 to saturate restriction factors was mainly due to their loss of interaction with TRIM5α. We, therefore, concluded that the ability of HIV-1 with SIVmac L4/5 and L6/7 to bind to TRIM5α is diminished in LLC-MK2 cells.
HIV-1 derivative with SIVmac L4/5, L6/7, and vif sequences can replicate efficiently in monkey primary cells
We created simian-tropic HIV-1 with more efficient replication capability in CM cells using the knowledge obtained from our previous study of TRIM5α and HIV-2 capsid sequence variations  Introduction of the entire SIVmac L6/7 CA into the previously constructed version of HIV-1 derivatives containing SIVmac L4/5 CA and vif  caused only a four amino acid change in CA but showed improved replication capability of HIV-1 in the CM cell line HSC-F. Introduction of the entire SIVmac L6/7 CA into NL-DT5R, which has two additional amino acid mutations in the env gene, enhanced replication in CD8+ cells-depleted CM PBMCs. After prolonged stimulation of CM PBMCs, replication of the original version of NL-DT5R was suppressed while that of NL-DT5R with SIVmac L6/7 was not. It would thus be of interest to test whether those HIV-1 derivatives with both L4/5 andL6/7 from SIVmac can induce infection of CM in vivo.
While the high-dose inoculation of WT HIV-1 particles into Rh cells saturated endogenous TRIM5α and enhanced subsequent infection with HIV-1, the introduction of HIV-1 particles that contained both L4/5 and L6/7 from SIVmac greatly impaired the ability of the particles to saturate TRIM5α. When we replaced either HIV-1 L4/5 or L6/7 with the corresponding sequence from SIVmac, these particles still saturated TRIM5α. These findings suggest that TRIM5α recognized the overall structure composed of both L4/5 and L6/7 of HIV-1 CA. Our previous results from computational 3D-structure modeling analysis of HIV-2 CA support this hypothesis . The 120th amino acid of HIV-2 CA, which affects viral susceptibility to TRIM5α restriction, was located in L6/7. It is especially worth noting that the amino acid substitution at the 120th position was previously predicted to induce marked changes in the configuration of L6/7 and the L6/7 with the CM TRIM5α-sensitive Pro positioned most closely to L4/5 of HIV-2 . It would, therefore, be interesting to investigate whether monkey TRIM5α proteins recognize CypA bound-L4/5 of HIV-1 CA.
During the preparation of our manuscript, Lin and Emerman reported that SIVagmTAN with both HIV-1 L4/5 and L6/7 was susceptible to Rh-TRIM5α restriction . Our result is consistent with their finding, since the HIV-1 particles with both SIVmac L6/7 and SIVmac L4/5 showed reduced saturation activity for TRIM5α in Rh cells compared with HIV-1 particles with SIVmac L4/5 alone. Hatziioannou et al. very recently reported that stHIV-1 strains, which differ from HIV-1 only in the vif gene, could efficiently replicate in pig-tailed monkey and proposed a pig-tail monkey model of HIV-1 infection . This is not surprising, since pig-tailed monkeys lack a TRIM5α protein, and the dominant form of TRIM5 expressed in this monkey species is a TRIMCyp fusion protein lacking anti-HIV-1 activity [46–48].
When we subjected CD8-depleted CM PBMC to prolonged stimulation, NL-DT5R6/7S grew efficiently but NL-DT5R did not. Since the expression levels of TRIM5α mRNA in human PBMC increased after stimulation with PHA and IL2 for 3 days (data not shown), we speculated that the higher expression levels of CM-TRIM5α in fully stimulated CM cells resulted in efficient restriction of NL-DT5R. However, no clear enhancement of CM TRIM5α mRNA expression could be detected in the CM cells subjected to prolonged stimulation (data not shown). The reason why NL-DT5R failed to grow in CM cells with prolonged stimulation is not yet clear, but it is possible that fully stimulated CM cells exerted stronger intrinsic inhibitory activity against HIV-1 infection than those with short-term stimulation.
NL-DT5R6/7S and NL-ScaVR6/7S replicated less efficiently in human MT4 cells than did the parental NL-DT5R and NL-ScaVR. One possible explanation is that the virus with SIVmac L6/7 became resistant to CM TRIM5α but became more sensitive to human TRIM5α, since the latter can restrict SIVmac more efficiently than HIV-1. Another possibility is that replacement of CA allowed the virus to evade the intrinsic inhibitory factors in CM cells but impaired viral replication per se.
We used the CM T cell line HSC-F and CD8+ cell-depleted PBMC from CM but not from Rh for our replication experiments. Although we observed an improvement of viral replication in CM cells, we cannot assume that the replacement of L4/5 and L6/7 is enough for HIV-1 to replicate to high titers in Rh cells since the CM TRIM5α resistant HIV-2 mutant virus GH123 (Q) was found to be restricted by Rh TRIM5α . NL-DT5R6/7S and NL-ScaVR6/7S also showed less efficient replication capability than did SIVmac (Fig. 1). We are currently trying to adapt these viruses to CM and Rh cells by means of long-term passaging in the hope of introducing compensating mutations that can overcome these disadvantages and further augment their replicative capabilities in human and simian cells to reach a similar level as seen with SIVmac.
We have succeeded in improving simian-tropic HIV-1 for more efficient replication in CM cells by introduction of the SIVmac L6/7 CA sequence. It will be of interest to determine whether the HIV-1 derivatives with SIVmac L4/5 and L6/7 can induce infection in cynomolgus monkeys in vivo. Even if they fail to do so, further modification and/or adaptation of the current version of simian-tropic HIV-1 in monkey cells might be expected to lead to the development of an HIV-1 infection model in OWMs. This model has been long-awaited as a tool for vaccine development and as a model for better understanding of AIDS pathogenesis.
old world monkey
HIV-1/SIV chimeric virus
peripheral blood mononuclear cell
green fluorescence protein
vesicular stomatitis virus glycoprotein
a loop between α-helices 4 and 5
a loop between α-helices 6 and 7.
The authors wish to thank Mss.Setsuko Bandou and Noriko Teramoto for their helpful assistance.
This work was supported by grants from the Health Science Foundation, the Ministry of Education, Culture, Sports, Science, and Technology, and the Ministry of Health, Labour and Welfare, Japan.
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