The highly polymorphic cyclophilin A-binding loop in HIV-1 capsid modulates viral resistance to MxB
© Liu et al.; licensee BioMed Central. 2015
Received: 29 September 2014
Accepted: 16 December 2014
Published: 9 January 2015
The human myxovirus-resistance protein B (MxB, also called Mx2) was recently reported to inhibit HIV-1 infection by impeding the nuclear import and integration of viral DNA. However, it is currently unknown whether there exist MxB-resistant HIV-1 strains in the infected individuals. Answer to this question should address whether MxB exerts an inhibitory pressure on HIV-1 in vivo and whether HIV-1 has evolved to evade MxB inhibition.
We have examined ten transmitted founder (T/F) HIV-1 strains for their sensitivity to MxB inhibition by infecting CD4+ T cell lines SupT1 and PM1 that were stably transduced to express MxB. Two T/F stains, CH040.c and RHPA.c, were found resistant and this resistance phenotype was mapped to the amino acid positions 87 and 208 in viral capsid. The H87Q mutation is located in the cyclophilin A (CypA) binding loop and has a prevalence of 21% in HIV-1 sequences registered in HIV database. This finding prompted us to test other frequent amino acid variants in the CypA-binding region and the results revealed MxB-resistant mutations at amino acid positions 86, 87, 88 and 92 in capsid. All these mutations diminished the interaction of HIV-1 capsid with CypA.
Our results demonstrate the existence of MxB-resistant T/F HIV-1 strains. The high prevalence of MxB-resistant mutations in the CypA-binding loop indicates the significant selective pressure of MxB on HIV-1 replication in vivo especially given that this viral resistance mechanism operates at expense of losing CypA.
Host restriction factors are important components of the antiviral defense. HIV research has led to the discovery of multiple restriction factors that not only inhibit HIV but also a wide range of other viruses. Examples of these restriction factors include APOBEC3G , Trim5α , tetherin [3,4], and SAMHD1 [5,6] (reviewed in ). A recent addition to this important family of proteins is human myxovirus-resistance protein B (MxB, also called Mx2). Despite the well-known antiviral property of MxA , no virus was known to be inhibited by MxB until 2011 when two screen studies showed that vesicular stomatitis virus (VSV), mouse herpesvirus type 68 (MHV-68) and HIV-1 could be restricted by MxB [9,10]. The anti-HIV-1 activity of MxB was further established by three independent studies which reported that MxB impedes HIV-1 DNA nuclear import and/or integration by targeting viral capsid [11-13]. A number of mutations in viral capsid were shown to render HIV-1 resistant to MxB, including N57S, G89V, P90A, N74D and others [12-15]. Furthermore, we identified in the escape viruses a capsid mutation A88T that overcomes MxB inhibition . These results suggested that HIV-1 was able to escape MxB restriction by mutating its capsid sequence. However, the aforementioned capsid mutations are absent in the HIV sequence database likely because they all cause severe defects in virus infectivity. We speculate that, if MxB does exert a strong inhibitory pressure on HIV-1 infection in vivo, then there should exist MxB-resistant HIV-1 strains.
Given the role of the viral capsid in countering MxB restriction [11-14], we aligned the capsid sequences of CH040.c and RHPA.c with that of NL4-3. Three amino acid positions in the capsid of both CH040.c and RHPA.c differ from those in NL4-3 capsid (Figure 1E). These are H87, H120 and G208 in NL4-3; Q87, N120 and A208 in CH040.c and RHPA.c. We next inserted Q87, N120 and A208 into NL4-3 capsid and generated mutations H87Q, H120N and G208A in order to determine which of these three amino acids lead to MxB resistance. None of these three mutations markedly affected the infectivity of NL4-3 (Figure 1F). When these NL4-3 mutants were tested in MxB-expressing SupT1 cells, H87Q and G208A, but not H120N, were refractory to MxB inhibition (Figure 1G).
We have previously shown that either knockdown of CypA or cyclosporine A (CSA) treatment to block CypA rescued HIV-1 infection of MxB-expressing SupT1 cells . We therefore asked whether the above capsid variants in the CypA-binding loop modulated HIV-1 susceptibility to MxB by altering the binding of CypA to the viral capsid. To answer this question, we transfected the wild type and mutated HIV-1NL4–3 DNA into HEK293T cells and purified HIV-1 particles by ultracentrifugation through a sucrose gradient . The presence of CypA in HIV-1 particles was examined by Western blotting and the results showed that the wild type NL4-3 and MxB-sensitive mutants I91V, M96I and M96L packaged substantial amounts of CypA as opposed to the MxB-resistant mutants V86A, V86Q, H87P, H87Q, A88V and A92P that packaged little or no CypA (Figure 2D). This data suggests that some HIV-1 strains have evolved to escape MxB inhibition at the expense of losing viral capsid binding to CypA.
In conclusion, we have identified two T/F HIV-1 strains that are resistant to MxB restriction in SupT1 and PM1 cells, and further mapped the resistant mutations to viral capsid. Our data also revealed the high prevalence of MxB-resistant mutations in the CypA-binding loop of the viral capsid. Since these MxB-resistant mutations diminish the association of viral capsid with CypA which acts as a host dependency factor for HIV-1, there is a cost for the virus to adopt this MxB-resistant pathway, which helps to explain why these MxB-resistant mutations have not prevailed the circulating HIV-1 strains. Together with the recent finding that the P207S, G208R and T210K mutations confer resistance to MxB , our data on the G208A mutation reinforces the importance of this region of capsid in modulating HIV-1 sensitivity to MxB. Considering that the A208 residue of capsid has a 35% prevalence rate in the circulating HIV-1 strains (http://www.hiv.lanl.gov/content/index), the G208A variant may serve a distinct mechanism, in addition to the variants in the CypA-binding loop, that HIV-1 employs to escape from MxB restriction in vivo.
We would like to thank Alexandre Sze for critical reading of the manuscript, Rongtuan Lin for valuable suggestions. HIV-1 transmitted founder viruses were obtained through the NIH AIDS Reagent Program. This research was supported by funding from Canadian Foundation for AIDS Research (CANFAR) and Canadian Institutes of Health Research (CIHR).
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