Variability in the P6gag domains of HIV-1 involved in viral budding
Holguín, África; Alvarez, Amparo; Soriano, Vincent
Service of Infectious Diseases, Hospital Carlos III, Madrid, Spain.
Received 17 October, 2005
Accepted 1 November, 2005
The genetic variability within PT/SAP, LYP and LXXLF HIV-1 P6gag motifs, required for the binding to Tsg101 and AIP1 cellular host proteins during viral budding, was examined in 122 HIV-infected subjects. PT/SAP duplications were statistically more frequent in B versus non-B subtypes. Substitutions at LYP were fourfold less frequent in antiretroviral-experienced only in clade B. P6gag variability across HIV-1 subtypes and after antiretroviral exposure may influence interactions with host cells involved in viral budding.
HIV and other retroviruses exit infected cells by budding from the plasma membrane . The virion then spreads extracellularly, infecting new susceptible cells. Budding is promoted by short and highly conserved motifs within the HIV-1 P6gag protein , providing interaction sites for the host cellular proteins Tsg101 [3,4] and AIP1 . Both cellular proteins are required for the adequate release of HIV-1 [6,7]. A tetrapeptide P(T/S)AP motif (residues 7–10) within HIV-1 P6gag is crucial for recruiting Tsg101 [8,9], and for the detachment of virions from the cell surface . The same peptide has been recognized in Ebola and HTLV-1 viruses [1,9,10]. The HIV-1 P6gag residues 32–46 are involved in the binding to AIP1, being LYP and LXXLF domains (residues 35–37 and 41–45, respectively) part of the AIP1 primary binding site .
Nine subtypes (A, B, C, D, F, G, H, J, K) and multiple intersubtype recombinant variants have been described within HIV-1 group M . Most information about the HIV-1 cell cycle derives from subtype B viruses, prevalent in north America and western Europe. However, non-B subtypes are responsible for more than 90% of the 40 million HIV-1 infections worldwide [12,13]. Any significant difference between distinct HIV-1 subtypes may have implications for HIV vaccine development, serological and genetic diagnosis [14,15], viral load measurement  and antiretroviral therapy [17–21]. In this study we have examined the P6gag region across clades in an attempt to explore whether differences exist between subtypes in interactions with host cell proteins involved in viral budding.
The genetic variability within PT/SAP, LYP and LXXLF HIV-1 P6gag motifs was examined in plasma specimens collected during the past 10 years from 122 HIV-1-infected individuals living in Spain, 82 of whom are drug naive. These specimens had previously been ascribed to different HIV-1 gag subtypes: 50A, 54B, 2C, 1F, 12G, 1H and 2U . P6gag sequences were deposited at the GenBank. The chi-square or Fisher's exact tests were used to detect significant differences between proportions. Comparisons were conducted using Epi Info version 6.02 (Centers for Disease Control and Prevention, Atlanta, Georgia, USA). Only P values below 0.05 were considered significant.
Earlier studies described specific patterns of insertions and deletions within P6gag across HIV-1 clades [22,23]. We found that insertions (from 3 to 9 amino acids) within P6gag were more frequent in subtype B compared with non-B subtypes (33% versus 4.4%; P = 0.0001), mostly (64%) being located nearby the PT/SAP motif (positions 7–10). Similarly, total or partial PT/SAP duplications were more frequent in clade B than in non-B strains (24% versus 1.5%; P < 0.001). The rate of P6gag insertions across subtypes did not differ significantly when comparing patients with and without exposure to antiretroviral therapy. This is in contrast to earlier reports [20,24,25], and according to others . For some authors these PTAPP duplications could be considered as natural polymorphisms . However, they could lengthen the Tsg101 binding site, and therefore these viruses might have an enhanced Tsg101 binding. Recent findings have suggested that PTAPP duplications could impact on the virus replicative capacity depending on the pol genetic context .
As HIV-1 budding cannot occur in the absence of Tsg101 , mutations that disrupt the Tsg101/Gag interaction typically inhibit HIV-1 release to a much greater extent than mutations that disrupt the AIP1/Gag interaction . Accordingly, we only found two out of 122 viruses (1.6%) from drug-naive individuals with substitutions within the PT/SAP motif. The first (accession number AY248409) had a clade B virus with a P10L substitution, known to disrupt the Tsg101 interaction, reducing virion release in vitro . It conserved the LYP motif and harboured a PTAPP insertion after the P11E change. This insertion could represent an additional binding site for the Tsg101 protein. The second specimen (accession number AY248370) was a clade G virus, with an A9T change within PT/SAP and a L35Q substitution at the LYP motif.
Despite similar rates of amino acid substitutions within the LYP motif in B and non-B viruses (27.8% versus 32.2%), a higher proportion of non-B than B subtypes presented two or more substitutions and deletions per specimen (29.4% versus 3.7%; P < 0.001). The LYP sequence was altered in clade C and H viruses, in 91% of clade A, and 80% of clade G. Conversely, it was conserved in clades J and F specimens, in 92% out of 39 recombinants AgagXpro, and in 67% of clade B viruses. P37 residue duplication at the LYP motif was present in 67.6% and 7.4% of non-B and B viruses, respectively (P < 0.0001), and could be considered a polymorphic change. The AIP1 binding site sequences carrying substitutions in the study population are shown in Table 1.
Interestingly, amino acid substitutions at the LYP motif were fourfold less frequent in clade B viruses from antiretroviral-experienced patients compared with drug-naive patients (9.5% versus 39.4%; P = 0.01). Restrictions imposed by drug resistance mutations selected in the pol gene could explain this finding. A similar influence of antiretroviral therapy on LYP variability was not recognized in non-B subtypes.
The deletion of residues 34–35 of P6gag has previously been associated with the disruption of the AIP1 binding site  and with non-progressive HIV-1 infection , Seven out of 122 viruses (5.7%) harboured amino acid deletions within the LYP P6gag motif (residues 35–37). Therefore, these viruses could have alternative sites for their interaction with the cellular machinery involved in viral budding.
The two leucines at the LXXLF motif (residues 41–45), required for AIP1 binding , were conserved in all 122 viruses, regardless of the HIV-1 subtype or antiretroviral exposure. A R42K substitution was observed in 90% of non-B and 50% of B viruses (P < 0.0001), most probably representing a polymorphism, because it is not critical for the AIP1 interaction.
In summary, we found high genetic variability in the HIV-1 P6gag region, including substitutions, deletions and insertions, which was influenced by subtype and antiretroviral exposure. It could affect the interaction between HIV-1 and Tsg101/AIP1 host proteins, modifying viral budding or favouring alternative budding pathways. Functional analyses are warranted to confirm our findings, particularly if there is an effect of antiretroviral treatment on the variability at Gag residues that might influence the virus replication capacity, as has previously been suggested [31,32], and whether it could occur in a subtype-dependent manner.
The authors wish to thank Juan Martinez-Serrano (Aaron Diamond AIDS Research Center, New York) for helpful comments.
Sponsorship: This work was supported in part by grants from Fundación Investigación y Educación en SIDA (IES), Ministerio de Ciencia y Tecnología (SAF2003-03551), Fondo de Investigaciones Sanitarias (FIS PI030004) and Red de Investigación en SIDA (RIS, project 173).
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