Membrane topology analysis of HIV-1 envelope glycoprotein gp41
The gp41 subunit of the HIV-1 envelope glycoprotein (Env) has been widely regarded as a type I transmembrane protein with a single membrane-spanning domain (MSD). An alternative topology model suggested multiple MSDs. The major discrepancy between the two models is that the cytoplasmic Kennedy sequence in the single MSD model is assigned as the extracellular loop accessible to neutralizing antibodies in the other model. We examined the membrane topology of the gp41 subunit in both prokaryotic and mammalian systems. We attached topological markers to the C-termini of serially truncated gp41. In the prokaryotic system, we utilized a green fluorescent protein (GFP) that is only active in the cytoplasm. The tag protein (HaloTag) and a membrane-impermeable ligand specific to HaloTag was used in the mammalian system.
In the absence of membrane fusion, both the prokaryotic and mammalian systems (293FT cells) supported the single MSD model. In the presence of membrane fusion in mammalian cells (293CD4 cells), the data obtained seem to support the multiple MSD model. However, the region predicted to be a potential MSD is the highly hydrophilic Kennedy sequence and is least likely to become a MSD based on several algorithms. Further analysis revealed the induction of membrane permeability during membrane fusion, allowing the membrane-impermeable ligand and antibodies to cross the membrane. Therefore, we cannot completely rule out the possible artifacts. Addition of membrane fusion inhibitors or alterations of the MSD sequence decreased the induction of membrane permeability.
It is likely that a single MSD model for HIV-1 gp41 holds true even in the presence of membrane fusion. The degree of the augmentation of membrane permeability we observed was dependent on the membrane fusion and sequence of the MSD.
KeywordsGreen Fluorescent Protein Membrane Fusion Membrane Topology Prokaryotic System 293FT Cell
List of abbreviations
human immunodeficiency virus type-1
lentiviral lytic peptide
green fluorescent protein
fetal bovine serum
Alexa Fluor 488
phosphate buffered saline.
The envelope glycoprotein (Env) of human immunodeficiency virus type-1 (HIV-1) plays a critical role in the early stage of HIV-1 infection. Env is synthesized as a precursor protein, gp160 [1, 2], and processed into gp120 and gp41 during transport from the endoplasmic reticulum to Golgi network [3, 4]. The gp120 subunit determines host range through its recognition of the receptor and co-receptor complex. The transmembrane protein gp41 mediates the membrane fusion between the host and viral membranes. It is composed of an ectodomain (extracellular domain), a cytoplasmic domain, and a transmembrane domain. The ectodomain has coiled-coil-forming heptad repeats essential for membrane fusion. The cytoplasmic domain contains three amphipathic helices called the lentiviral lytic peptide (LLP) 1, 2 and 3. The LLP-1 and LLP-2 portions have a high hydrophobic moment common to membrane-lytic peptides [5, 6, 7, 8, 9].
On the other hand, the mapping of the epitopes for neutralizing antibodies called into question the single MSD model. Some of the epitopes were mapped to the cytoplasmic region which contained the amino acid sequence known as the Kennedy sequence (724PRGPDRPEGIEEEGGERDRDRS745)[14, 15, 16] (Figure 1A). Furthermore, a report using an antibody raised against the LLP-2 portion revealed target binding during membrane fusion when added extracellularly . As antibodies in general are not expected to cross intact membranes, an alternative membrane topology model of gp41 has been suggested in order to assign the mapped epitopes in the extracellular region  (Figure 1C). In this alternative model multiple MSDs were proposed because the C-terminus was assumed to be in the cytoplasm. Furthermore, the transmembrane portion of the single MSD model is expected to cross the membrane twice and one of LLPs, LLP2, is a putative third MSD (Figure 1C).
Several studies of the transmembrane portion of the single MSD model showed that it plays a critical role in the modulation of the membrane fusion process, which is an essential step of the HIV-1 life cycle [18, 19, 20, 21, 22, 23, 24]. Therefore analysis of the topology and structures of the transmembrane domain of gp41 is critical for our understanding of the mechanism of the membrane fusion. Furthermore the location of the neutralizing epitopes for antibodies is vital for a vaccine development.
In this study we reexamined gp41 topology in two different biological systems; prokaryotic and mammalian systems. The results of prokaryotic and mammalian systems without membrane fusion supported the single MSD model. The results obtained in the mammalian system in the presence of membrane fusion seem to support a transient alteration of the membrane topology of gp41. It is important, however, to note that the effect of the induction of membrane permeability during HIV-1 Env-mediated membrane fusion cannot be excluded. The induction of membrane permeability was reduced by replacing the HIV-1 MSD with that of a foreign protein, CD22.
All PCR amplicons were first cloned into pCR4Blunt-TOPO using the TOPO cloning kit (Invitrogen, Carlsbad, CA) and sequences were verified.
Plasmids used in this study
For prokaryotic system
Multiple cloning site-modified pMalp2e containing Kan R and Green fluorescent protein genes
mpKMalp2e-GFP with C-terminally truncated gp41 at W666
mpKMalp2e-GFP with C-terminally truncated gp41 at I682
mpKMalp2e-GFP with C-terminally truncated gp41 at G694
mpKMalp2e-GFP with C-terminally truncated gp41 at R725
mpKMalp2e-GFP with C-terminally truncated gp41 at R747
mpKMalp2e-GFP with C-terminally truncated gp41 at R788
mpKMalp2e-GFP with C-terminally truncated gp41 at A819
mpKMalp2e-GFP with full-length gp41
Modified pET-47b with modified super folder GFP
For mammalian system
The CMV promoter driven mammalian expression vector containing HaloTag gene
pHIVenv-Halo containing Env with C-terminally truncated gp41 at R725
pHIVenv-Halo containing Env with C-terminally truncated gp41 at R747
pHIVenv-Halo containing Env with C-terminally truncated gp41 at R788
pHIVenv-Halo containing Env with C-terminally truncated gp41 at A819
pHIVenv-Halo containing full-length Env
The gp41 MSD replaced pHIVenv-gp41-5 with the MSD of CD22
The gp41 MSD replaced pHIVenv-gp41-8 with the MSD of CD22
The expression vector of the GPI anchored-HaloTag
The expression vector of Tac antigen of IL-2 receptor fused with C-terminal HaloTag
pKcTacHalo vector whose HaloTag was replaced with 3xFLAG
Expression of GFP-fused gp41 proteins and measurement of GFP fluorescence intensity
E. coli strain BL21 transformed with mpKMal-p2e carrying serially truncated gp41 genes fused to GFP reporter was grown overnight at 22°C in TAG medium (10 g/L Tryptone, 5 g/L NaCl, 5 g/L Glucose, 7 g/L K2HPO4, 3 g/L KH2PO4, 1 g/L (NH4)2SO4, 0.47 g/L Sodium Citrate) with 50 μg/ml kanamycin. The overnight bacterial culture was diluted 1:50 in 4 ml TAG fresh medium containing 50 μg/ml kanamycin and growth was continued at 22°C until the OD600 reached 0.2. Cells were grown for overnight in the presence of 0.1 mM IPTG. Subsequently, one ml aliquot of culture was collected and resuspended in 0.5 ml of PBS buffer and the GFP fluorescence intensity was measured by flow cytometry using a FACS Calibur (BD Biosciences, Mississauga, ON). At the same time, another 1 ml aliquot of culture was dispensed for SDS-PAGE and immunoblotting analysis.
Mammalian cell culture, transfection, labeling, and imaging
The 293FT cells (Invitrogen, Carlsbad, USA) or 293CD4 cells (293 cells constitutively expressing human CD4)  were grown in 96-well Matriplates (GE Healthcare, Piscataway, NJ) with Dulbecco's modified Eagle medium (DMEM; Sigma, St. Louis, USA) supplemented with 10% FBS (Hyclone Labs., Logan, UT). In the case of 293FT, 5 μg/ml Geneticine (GiBco, Grand Island, USA) was further supplied. Cells were grown at 37°C in 5% CO2 incubator.
DNA transfection of mammalian cells was performed using Fugene HD (Roche, Indianapolis, USA; Fugene HD (μl): DNA(μg): DMEM(μl) = 5:2:200). The transfection mix was incubated for 15 mins at room temperature prior to addition to the cell culture in a drop-wise manner (10 μl per well). After certain hours of transfection the transfected cells were subjected for further analyses as described below.
At the indicated time after transfection, the transfected cells were probed with HaloTag ligands. The starting time point of labeling after transfection was different for different experiments involving a different set of cells and vectors (see the Results section). The labeling was performed as suggested by the manufacturer (Promega). Briefly, the transfected live cells were labeled for 15 mins at 37°C with 1 μM of HaloTag ligand Alexa Fluor 488 (AF488), a membrane-impermeable ligand, or Oregon Green (OG), a membrane permeable ligand, respectively. After labeling, the cells were rinsed three times with 200 μl prewarmed DMEM plus 10% FBS and subsequently incubated at 37°C with 5% CO2 for 30 mins. The medium was changed with fresh warm DMEM plus 10% FBS, then images were captured using a confocal microscope (Olympus FluoView FV1000, Tokyo, Japan).
Immunofluorescent staining assay using the anti-FLAG monoclonal antibody (Sigma) was performed to detect the FLAG-tagged proteins as below. Following the fixation of the transfected cells with 2% paraformaldehyde at 25°C for 5 mins, the anti-FLAG antibody (1/200 in 0.5% BSA and PBS) was used as the first antibody. After incubating at room temperature for 1 h, the cells were rinsed 3 times with 200 μl prewarmed PBS plus 0.5% BSA and subsequently incubated with anti-mouse antibody conjugated with AlexaFluor 488 (Invitrogen) (1/200 in 0.5% BSA and PBS) at room temperature for 1 h. The images were captured using a confocal microscope (Olympus).
To evaluate the cell viability, staining with propidium iodide (PI)  was used. In the case of co-labeling with the HaloTag ligands, staining with AF488 was performed first, then PI staining for 15 min at room temperature with a final concentration of 2.5μg/ml followed. The cells were rinsed two times with PBS and images were analyzed as described above. In the case of co-staining with anti-FLAG monoclonal antibodies, PI staining was performed first, followed by labeling with the anti-FLAG monoclonal antibody.
To mimic the effect of the conformational changes of gp120 after its binding to the CD4 receptor, soluble CD4 was added to the 293FT cells transfected with HIV-1 Env expression vectors. The soluble CD4 protein (final concentration: 0.1 μM) was kept in the medium since immediately after transfection.
Syncytia formation assay
A syncytia formation assay was performed by transfecting the HIV-1 Env expression vectors (listed as For mammalian system in Table 1) into the 293CD4 cells. The cells were transfected when they were about 50% confluent. At 48 h after transfection, the images were captured with IN Cell analyzer 1000 (GE Healthcare, Uppsala, Sweden). The fusion activity of Halo-fused Env was evaluated by counting 300 nuclei in total after staining with 2 μM Hoechst and determining the percentage of nuclei included in syncytia.
Bacterial cultures (1 ml) were harvested and resuspended in 50 μl SDS-PAGE loading buffer (2% SDS, 2 mM DTT, 10% glycerol, 50 mM Tris-HCl, pH6.8, 0.01% Bromo phenol blue). The mixture was kept for 10 mins at 95°C and subjected to centrifugation (20,000 g, 4°C) with MX-301 (Tomy, Japan) to remove the pellets. Whole cell lysates (2 μl) were resolved using a 5-20% gradient SDS polyacrylamide gel (DRC, Tokyo, Japan). The proteins were transferred to the PVDF membrane and probed with 15,000-fold diluted anti-GFP antibody (Santa Cruz Biotechnology, Santa Cruz, USA) for 1 h at room temperature. Anti-mouse antibody (GE healthcare), diluted by 5,000-fold, was used as the secondary antibody. The signal was developed by streptavidin-biotinylated horseradish peroxidase complex (GE healthcare) and the chemiluminescence reagents (Roche), and detected by LAS3000 (Fuji).
The transfected 293FT cells grown in 10-cm dishes as described above were collected and centrifugated (5,000 g, 4°C) with MX-301. The cell pellet was lysed with 250μl of RIPA lysis buffer [50 mM Tris-Cl (pH 7.4), 150 mM NaCl, 1% NP-40, 0.1% SDS] and then centrifuged (MLA-130 rotor, 100,000rpm, 30 mins, 4°C) with Beckman Optima™Max Ultracentrifuge. The supernatant (20 μl) was treated with the same method as described above. The protein bands on the PVDF membrane were developed as described above, except for the 500-fold diluted anti-Halo pAb (Promega) and 5000-fold diluted anti-rabbit antibody (GE healthcare) which were used as the primary and secondary antibodies, respectively.
Topology mapping of gp41 using GFP as a reporter in a prokaryotic system
We first employed the well-established prokaryotic topological analysis using GFP as a reporter [31, 32]. If GFP is located in the cytoplasm it folds into an active form, whereas when it is translocated into the periplasm it is non-functional . The periplasm-targeted maltose-binding protein was placed at the N-terminus of the gp41 portion to be tested, and then GFP, a topological reporter, was fused to the C-terminus of the gp41 fragment (Figure 2A). The series of gp41 proteins truncated at the different C-terminal positions were tested (Figure 1A and Table 1). The N-terminus of gp41 portion included was fixed at the position of 636th amino acid close to the predicted MSD (Figure 1A dotted line), because there is little controversy on the beginning of the MSD itself.
Results of GFP quantification
Adjusted GFP signal
(The number of counts
Expression of HaloTag-attached HIV-1 Env in mammalian cells
Although the bacterial system is quick and informative, eukaryote specific post-translational modifications and/or the difference in the composition of lipids in the membrane may affect the topology of gp41. Therefore, HIV-1 Env with the C-terminus of gp41 linked to HaloTag was expressed in mammalian cells (Figure 3A). The HaloTag is a 33 kDa protein designed to covalently bind to its membrane-permeable/impermeable ligands conjugated with a fluorescent chromophore . Based on the previous published results  and our own results of the prokaryotic system (see above), we focused on the analysis of the region after the predicted MSD of the single MSD model (truncation positions 4-8 in Figure 1A). The GPI-anchored HaloTag protein (Halo-GPI) and the HaloTag attached to the C-terminus of the Tac antigen after MSD (Tac-Halo) were made as the controls for the extracellular and intracellular positioning of HaloTags, respectively (Figure 3A and Table 1). Expression of HaloTag-attached envelope proteins was confirmed by immunofluorescence analysis with anti-gp120 antibody (data not shown) and immunoblotting analysis with anti-Halo antibodies (Figure 3B). The bands around 130-170kD and 40-55kD for pHIVenv-gp41-Halo are HaloTag-attached gp160 and gp41, respectively.
The membrane fusion capacity of these mutants was examined with a syncytia formation assay by transfecting the expression vector into 293CD4 cells . Although the efficiency of the fusion was reduced in all of the HaloTag-attached envelope proteins, all still retained membrane fusion activity (Figure 3C). When we analyzed the fusion activity with the DSP assay , better fusion was observed (data not shown). Since the DSP assay relies on the smaller reporter proteins, the presence of the defect of pore dilatation in HaloTag attached mutants was suggested.
Topology mapping of gp41 in mammalian cells using HaloTag-specific membrane-impermeable ligands
Examination of membrane topology with HaloTag in syncytia formed in 293CD4
When the 293CD4 cells transfected with pHIVenv-gp41-5-Halo were stained with the anti-HaloTag antibody without permeabilization procedure, rare events of staining were observed (data not shown). These results suggest that the possibility of sporadic exposure of cytoplasmic domain of gp41 during membrane fusion with pHIVenv-gp41-5-Halo.
Augmented membrane permeability by Env-induced membrane fusion
Computational analyses of possible transmembrane domain
Region of the predicted membrane-spanning segment
Augmented membrane permeability is dependent on MSD sequence
Since membrane permeability was induced in the cells transfected with pHIVenv-gp41-5-Halo, the presence of LLPs is not required for the increased permeability. To further characterize the region required for this enhanced permeability we constructed the mutants in which the original gp41 MSD was replaced with the foreign MSD derived from CD22  in the pHIVenv context. Previous reports indicated that the MSD derived from CD22 did not alter the function of HIV-1 Env ; however, the replacement seemed to delay the appearance of syncytia when compared with the wild type (see below). We compared these mutants with the HIV-1 Env with the native MSD. In the case of the HIV-1 Env with its native MSD, intracellular HaloTag was detectable with membrane-impermeable AF488 at the earlier time point after co-transfection (16 h post transfection, Figure 7; pHIVenv- gp41-5 and 8). On the other hand, there was minimal staining in cells co-transfected with HIV-1 Env with CD22 MSD at 16 h after transfection (data not shown). At 44 h post transfection when the cells transfected with the native gp41 MSD were almost gone due to the cell death, some cells transfected with CD22 MSD mutants were stainable with AF488 (Figure 7 -C34, pHIVenv-CD22-gp41-5 or 8 + pKcTac-Halo). Therefore there is a significant difference in the pattern of the staining between the native and CD22 MSDs. At 44 h post transfection, there were more dead cells as indicated by the positive PI staining. These cells were also stained with AF488. There are, however, some syncytia stained only with AF488 for CD22 MSD mutants (Figure 7). Inhibition of the membrane fusion with C34 blocked the staining (Figure 7 +C34). Similar results were obtained if anti-FLAG antibodies were used to detect the FLAG tag located in the cytoplasm. (Figure 8 pHIVenv-CD22-gp41-5 or 8 + pKcTac-FLAG). Taken together, these results indicated that the induction of permeability was membrane fusion-dependent and that the gp41 MSD played some role in the degree of induced permeabilization during membrane fusion.
In this study we examined the membrane topology of the gp41 subunit in two different biological systems. The truncated gp41 subunit was tagged with the topological reporter protein at the C-terminus (Figure 1, 2, 3). A prokaryotic reporter, GFP [31, 32] and mammalian reporter, HaloTag , were used. Both reporters enabled us to examine the topology in living cells without the artifacts caused by fixing.
In our prokaryotic system, all of the tested constructs (mpKMalp2e-gp41-4, 5, 6, 7- and 8-GFP) showed stronger GFP fluorescence than the control. This suggested that gp41 had a single MSD that places the Kennedy sequence, LLP-2, LLP-3, LLP-1 and the C-terminus of gp41 in the cytoplasmic side. The analysis with β-lactamase, another topology reporter, which is only active in periplasm produced the data consistent with that of GFP (data not shown). These data are consistent with the results obtained by the currently available several programs for prediction of transmembrane domains (Table 3).
Our analysis of gp41 topology in mammalian cells without membrane fusion (293FT cells) supported the single transmembrane model, concordant with that of the prokaryotic system. Only sporadic staining with membrane impermeable ligands was observed for pHIVenv-gp41-5-Halo (truncation at position 747 in HXB2 Env) in fusion-competent 293CD4 cells. Since staining for the preceding truncation point, pHIVenv-gp41-4-Halo (truncation at the residue 725 in HXB2), was negative, suggesting an additional MSD between the residue 725 and 747. This region contains about 20 mainly hydrophilic amino acid residues that correspond to the Kennedy sequence. As shown in Table 3 no MSD was predicted in this region by several computational algorithms. So we speculated that there is other reason for the observed apparently contradictory observations.
We examined the possibility of enhanced membrane permeability to account for the staining of putative intracellular regions during membrane fusion. The intracellularly located HaloTag was labeled using the membrane-impermeable ligand for HaloTag when HIV-1 Env-mediated membrane fusion occurred (Figure 7). Antibodies were also able to stain the intracellular targets in conditions of membrane fusion (Figure 8). Although we cannot completely exclude the possible alternations of the gp41 topology, the multiple MSD model based on the epitope mapping [16, 17] needs to be reevaluated carefully given the increased permeability we have observed.
We attempted to map the region(s) of gp41 responsible for increased membrane permeability. Our data suggested that the increased permeability was dependent on active membrane fusion (Figure 7 and 8). It is consistent with several reports of the fusion-dependent induction of membrane permeability in HIV-1 infected cells [35, 36, 37, 38]. It is known that the several isolated subdomains of gp41, critical for membrane fusion, have potential to permeabilize the mammalian and the bacterial membranes [39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]. These include the fusion peptide, the membrane proximate external region, the MSD and the LLPs. Our data of pHIVenv-gp41-5 (Figure 7 and 8) excludes the possibility of the role of LLPs. Our data using MSD replacement mutants pHIVenv-CD22-gp41-5 or pHIVenv-CD22-gp41-8, suggested the MSD affected the level of permeability, but whether the MSD directly affected the permeability or the effect was mediated via the efficiency of the membrane fusion was hard to be determined.
Since our assay relied on the topological reporter proteins attached at the C-termini of truncated gp41 proteins, the possibility of artifacts cannot be excluded. The exact reason why neutralizing epitopes mapped to the cytoplasmic regions remains unclear. There are at least two possible explanations. First, it is possible that the some of the antibodies themselves are intrinsically membrane permeable. Second, permeability that is sufficient to permit antibodies to cross the membrane may be induced by membrane fusion. Although our findings support the latter model, further study is needed to explore whether an alternative topology for gp41 MSD during membrane fusion really takes place and if such a possibility is a general phenomenon for other HIV-1 strains.
The membrane topology of the gp41 subunit of HIV-1 Env was examined in both prokaryotic and mammalian systems. The topology with a single MSD was supported in both systems. In addition, augmented membrane permeability was shown to be dependent on both the sequence of MSD and active membrane fusion.
This work was supported by a contract research fund from the Ministry of Education, Culture, Sports, Science and Technology for Program of Japan Initiative for Global Research Network on Infectious Diseases. We thank Dr. Kunito Yoshiike for his critical reading of the manuscript.
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