Dual effect of the SR proteins ASF/SF2, SC35 and 9G8 on HIV-1 RNA splicing and virion production
© Jacquenet et al; licensee BioMed Central Ltd. 2005
Received: 02 May 2005
Accepted: 22 May 2005
Published: 22 May 2005
In HIV-1 infected cells transcription of the integrated provirus generates the single full length 9 kb viral RNA, a major fraction of which is spliced to produce the single-spliced 4 kb RNAs and the multiple-spliced 2 kb RNAs. These spliced RNAs are the messengers for the Env glycoproteins and the viral regulatory factors. The cellular SR and hnRNP proteins were shown in vitro to control alternative splicing by binding cis-regulatory elements on the viral RNA. To better understand in vivo the role of the SR proteins on HIV-1 genomic RNA splicing and virion production, we used a human cell line expressing high levels of complete HIV-1 and either one of the ASF/SF2, SC35, and 9G8 SR proteins. Results show that over-expressing SR proteins caused a large reduction of genomic RNA and that each SR protein modified the viral 9 kb RNA splicing pattern in a specific mode. In fact, ASF/SF2 increased the level of Vpr RNA while SC35 and 9G8 caused a large increase in Tat RNA. As expected, overexpressing SR proteins caused a strong reduction of total Gag made. However, we observed by immuno-confocal microscopy an accumulation of Gag at the plasma membrane and in intracellular compartments while there is a dramatic reduction of Env protein made in most cells. Due to the negative impact of the SR proteins on the levels of genomic RNA and HIV-1 structural proteins much less virions were produced which retained part of their infectivity. In conclusion, SR proteins can down-regulate the late steps of HIV-1 replication.
HIV-1 splicing regulation relies on the presence of (i) suboptimal splice sites [5, 6], (ii) exonic and intronic cis-acting elements [7–15] and (iii) trans-acting factors (generally hnRNPs and SR proteins) that mediate their effects by binding these elements [16–19]. SR proteins belong to a conserved family of structurally and functionally related phosphoproteins (for review, ref. ). These proteins participate in constitutive splicing by causing stabilizing interactions with components of the splicing machinery and are able to influence the choice of splicing sites in alternative splicing (for review see ref. ). The high level of conservation of the splicing pattern in different HIV expressing cells suggests that splicing regulation is critical for efficient virus replication [2, 21, 22]. Because SR proteins ASF/SF2, SC35, 9G8 and SRp40 have been shown to cause an imbalance in the HIV-1 splicing pattern in vitro and ex vivo [19, 23–26], we investigated the impact of SR protein over-expression on virus production and infectivity in a human cell line expressing infectious HIV-1.
In the present study we show that overexpression of one of the three SR proteins ASF/SF2, SC35 and 9G8 together with HIV-1 strongly affected the full length viral RNA splicing pattern, notably resulting in a strong reduction of the genomic RNA and Env mRNA levels. As a consequence, only small amounts of viral particles were produced which, however, retained part of their infectivity.
SR proteins alter the splicing pattern of HIV-1
Relative levels of the three viral mRNA classes. The amounts of radioactivy in mRNA signals identified by Northern blotting or by slot blotting experiments (see methods) were measured using a Storm scanner. (A) Relative levels of total intracellular viral RNA were determined as the sum of the radioactivity in the 3 signals corresponding to the 2, 4 and 9 kb mRNAs from the same experiments. Levels are expressed as the percentages of total viral RNA in cells transfected with HIV pNL4.3 only used as a reference (100 %) or with HIV-1 pNL4.3 and an SR plasmid. For the same degree of DNA transfection, the percentages of the unspliced and spliced mRNAs were calculated relative to the total viral RNA considered as 100 %. (B) Values of genomic RNA packaged into a standardized amounts of virions (CAp24 ELISA) are reported relative to the virions produced in the absence of SR protein overexpression (100%).
+ ASF/SF2 (%)
+ SC35 (%)
+ 9G8 (%)
Alterations of HIV-1 splicing pattern by SR proteins modify viral protein synthesis
The profound modifications of the HIV-1 splicing pattern by overexpression of one of the SR proteins were expected to strongly influence viral protein synthesis. Since the unspliced viral RNA serves both as the mRNA for Gag and Gag-Pol synthesis and as the pregenome, we expected the levels of Gag and newly made virions to be strongly reduced by the SR proteins. To this end, levels of intracellular HIV Gag were assessed by CAp24 ELISA on cell lysates 48 h after DNA transfection (see methods). To measure the levels of virion production, culture supernatants were harvested every day for two days, pooled, clarified by filtration and ultracentrifuged through a 20 % sucrose cushion. Pelleted viral particles were resuspended in TNE buffer (see methods) and virus production was monitored by CAp24 ELISA. Series of measurements indicated that ASF/SF2 and SC35 caused about a 10–12 fold reduction of total Gag synthesized while 9G8 reduced it by roughly 4 fold. These results are in agreement with the relative levels of the unspliced viral RNA in HIV-1 producer cells (Table 1A).
A large fraction of the 4 kb mRNAs codes for Env. The very low level of Env glycoproteins present in cells is consistent with the fact that SR proteins strongly reduced the encoding viral mRNA (Figure 2B; Figure 3B bottom panel).
Last we analysed viral protein synthesis directed by the multiple spliced 2 kb mRNAs, coding for the regulatory proteins Nef and Vpr and the trans-acting factors Tat and Rev. Only the expression of Vpr was found to be markedly enhanced by ASF/SF2 in agreement with the increased level of Vpr mRNAs (Figure 2; Figure 3B, compare lanes 1 and 2; and data not shown).
Thus we can conclude that the SR proteins have a strong indirect impact on viral protein synthesis due to their alterations of the HIV-1 splicing pattern. Only the rather high level of cell-associated Gag appears to contradict this view (see discussion).
Influence of the SR proteins on Gag and Env expression analysed by immuno-confocal microscopy
Overexpressing ASF/SF2 as evidenced by a blue nuclear staining in most cells (Figure 4B) caused a drastic reduction of Env but only moderately affected Gag (Figure 4B, green and red stainings) in agreement with the western blot data (Figure 3B, lane 2). As above, Gag was seen to accumulate in intracellular vesicles and at the plasma membrane while Env was expressed in a heterogeneous manner and mainly located in the cell interior (Figure 4B, HIV Env panel), probably in the Golgi area and in intracellular vesicles (Figure 4B, merge picture). Quantitative values on 100 cells, taking into account that 70–75% of the cells were positively transfected, showed that co-expression of Gag and ASF was observed in 25% of the cells while Gag, Env and ASF was seen in only 10% of the cells. At the same time 65% of the cells expressed ASF only (Figure 5, bars labelled ASF). These results further showed that the ASF/SF2 SR protein can have a drastic negative impact on HIV-1 since its overexpression caused a nearly complete suppression of Gag and Env expression in a large fraction of the cells (Figures 4B &5). SC35 (Figure 4C) and 9G8 (not shown) SR proteins had less pronounced effects since a majority of the cells coexpressed Gag and one SR protein (Figure 5; 45 to 55 % see bars labelled gag+SC35 and gag+9G8, respectively) or evenly in the case of Gag, Env and 9G8 (Figure 5; see bar labelled gag+env+9G8). These observations suggest that the SR proteins can have differential effects on HIV-1 structural protein expression.
The influence of the SR proteins on Gag and Env synthesis was further evaluated with respect to virion production and infectivity.
Influence of SR proteins on virion production and infectivity
Protein composition of the virions generated by cells overexpressing one of the SR factors, at a HIV-1/SR DNA ratio of 1:0.5, was investigated by western blotting using antibodies against the major core component, CAp24, the RT enzyme, viral factor VPR and the envelope glycoprotein TMgp41. As shown in Figure 6B, CAp24 and RT were found as processed Gag protein and Pol enzyme, respectively, in proportions similar or close to wt HIV-1 particles (see panels labelled αCAp24 and αRT). On the contrary, VPR was more abundant in virions upon overexpression of ASF/SF2 in agreement with higher levels of the corresponding viral mRNA and protein in cells (Figures 2 and 3B lane 2). With SC35 and 9G8 Vpr was hardly detected in virions in agreement with the very low level of Vpr mRNA and protein in cells (Figure 3B lanes 3–4). All SR proteins examined negatively impacted on the incorporation of Env TMgp41 in virions (Figure 6B, lanes 2–4), again in agreement with the fact that Env mRNA and protein levels were drastically reduced in cells (Figures 2 and 3B).
To test whether the decreased level of cellular unspliced viral RNA also caused an attenuation of genome packaging into newly made virions, viral particles corresponding to the same amounts of CAp24 were used to purify the genomic RNA which was analyzed by slot-blotting using a gag-specific probe. For all overexpressed SR proteins, genomic RNA packaging was reduced from 3 to 4 fold compared with control virions (Table 1B).
To determine the infectivity of virions produced by cells overexpressing one of the SR proteins, the same amount of virus-associated genomic RNA was used to infect Hela P4 cells, a HeLa subtype that constitutively expresses the CD4 receptor and contains the lacZ gene under the control of the HIV-1 LTR. One day later, blue cells were counted allowing us to assess virus infectivity (see methods). Upon overexpression of each one of the SR proteins, virus infectivity, based on the same amount of genomic RNA, was found to be 30 to 60% of the control virus, or 6 to 12 fold less based on identical amounts of CAp24-associated particles.
It can be concluded that overexpression of each one of the SR proteins caused a strong reduction of the unspliced viral RNA in cells, and this had a more pronounced effet on virion production than on Gag synthesis (Figures 2, 3, 4, 5, 6). At the same time levels of genomic RNA packaged into progeny virions remained high (Table 1). These findings are in full agreement with the fact that the genomic RNA is considered to be an indispensable partner of Gag in the course of virus assembly.
In the present study, we show that the overexpression of either one of three different SR proteins, namely ASF/SF2, SC35 and 9G8, profoundly affected the HIV-1 splicing pattern (Figure 1) , resulting in a drastic decrease of virus production. However, the progeny virions still made retained part of their infectivity. SR protein overexpression caused an oversplicing of the HIV-1 full length transcript and confirm that the targets of activation depend on the SR protein overexpressed. Indeed, ASF/SF2 stimulates splicing at sites A1 and A2, while SC35 and 9G8 preferentially enhance splicing at site A3 (Figures 1, 2). In addition to being general activators of constitutive splicing, results reported here confirm that each one of the three SR proteins exerts specific effects on the alternative splicing of HIV-1 primary RNA transcript (Figure 2) .
Little is known about the HIV-1 A1 site. Here, we show that ASF/SF2 participates in the utilization of A1 by a mechanism that requires further investigations. Many elements act in concert to repress splicing at site A2 such as its intrinsic weakness [5, 6] and the existence of the hnRNP A/B dependent ESSV located in the noncoding exon flanking sites A2 and D3 [8, 9]. Then how does ASF/SF2 exert this control ? The exon bridging hypothesis proposes that U1 snRNP binding to the downstream donor site acts to increase splicing efficiency at the upstream flanking acceptor site (for review see ). Also, SR proteins are known to stabilize U1 snRNP binding on suboptimal donor sites. Consequently, one can imagine that ASF/SF2 reinforces splicing at site A2 by stabilizing spliceosomal interactions at the suboptimal site D3. Accordingly, other SR proteins like SC35 or 9G8 would be expected to have the same effect as ASF/SF2 on site A2 and thus on Vpr mRNA synthesis. This prediction is inconsistent with our data (Figure 3) since overexpression of SC35 and 9G8 did not increase Vpr RNA level. Another possibility is that ASF/SF2 positively regulates splicing at site A2 by counteracting the effect of ESSV. ESSV represses splicing at site A2 by binding cellular hnRNP A/B proteins [8, 9]. This binding prevents the assembly of U2AF on the polypyrimidine tract (PPT) and subsequently the formation of a functional spliceosome between sites D1 and A2 . SR proteins are thought to also activate weak acceptor sites by facilitating the recruitment of U2AF on the PPT . It is tempting to speculate that the ratio between hnRNP A/B and ASF/SF2 bound close to site A2 modulates the binding of U2AF at this site. This effect of SR proteins is generally mediated by a splicing enhancer, but whether an ASF/SF2-dependent splicing element is required here remains to be determined.
Site A3 is used to generate Tat mRNAs. Like A2, A3 is intrinsikly weak and repressed by hnRNP A/B-dependent ESS2 and hnRNP H-dependent ESS2p [17, 29]. Our results show that a strong positive control is exerted by SR proteins SC35 and 9G8 at this level. Findings on SC35 are consistent with the recent data of Zahler et al.  reporting a novel ESE downstream of A3 that reinforces A3 utilization in the presence of a high level of SC35 in vitro. In addition, hnRNPs act in a trans-dominant manner to counteract that of SC35 in vitro . Taken together these results strongly suggest that changing the hnRNP/SC35 ratio probably leads to activation or repression of splicing at site A3. Little is known on the implications of SR protein 9G8 in HIV-1 splicing. The present data show that 9G8 appears to function in a way similar to SC35 (Figure 2). As for ASF/SF2, the exon bridging hypothesis can be mentioned but 9G8 acts mainly by binding specific cis-acting RNA elements . Even if overexpression of SC35 and 9G8 caused a large accumulation of Tat mRNAs, it is likely that these two SR proteins act by distinct mechanisms. Indeed, firstly SELEX experiments showed that 9G8 and SC35 recognize different consensus RNA sequences . Secondly, ESS2 mutations that in vitro strongly reinforce the binding of SC35 on an ESS2-containing transcript have no effect on 9G8 binding to the same substrate [19, 30]. Sequences important for 9G8 splicing activation remain to be determined.
In conclusion, the exact molecular mechanisms by which high levels of SR proteins cause a strong enhancement of genomic RNA splicing and consequently a severe inhibition of HIV-1 virion production remain to be determined. This is presently under investigation.
As expected, the profound changes of the HIV-1 splicing pattern caused by the overexpression of one of the SR proteins ASF/SF2, SC35 or 9G8 inhibited viral protein synthesis, notably that of the structural proteins Gag and Env (Figures 3, 4, 5) and consequently, virion production (Figure 6A). Still in agreement with such alterations of the HIV-1 splicing pattern (Figures 1, 2), Vpr synthesis was upregulated by ASF whereas SC35 and 9G8 had an opposite effect (Figure 3B). But it was surprising to find a rather high heterogeneous level of cell-associated Gag (Figure 3A). To explain this apparent discrepancy, one should remember that the unspliced viral RNA performs two essential functions, firstly as the mRNA for Gag and Gag-Pol synthesis and secondly as the pregenome for Gag assembly (reviewed in ref. ). In fact, the Gag assembly process requires two platforms that are the genomic RNA through specific NC-genomic RNA interactions [31, 32] and a cellular membrane in which Gag is anchored via MA-membrane interactions (reviewed in ref. ). Membranes are not limiting whereas the full length RNA is probably limiting due to its mobilization by the translating ribosomes (reviewed in ref. ). Actually, the fate of the full length viral RNA appears to result from a subtle balance between Gag translation on ribosomes and core assembly governed by Gag-genomic RNA interactions (reviewed in refs [31, 35]). In the presence of high amounts of the SR proteins, the unspliced viral RNA is even more limiting and thus probably rarely available for assembly. Hence, the cell-associated Gag corresponds to newly made free Gag molecules as well as Gag in newly assembled core nucleocomplexes which accumulate in the cell (Figure 4) before being released. According to this scheme of virus assembly, the low levels of the pregenomic RNA (Table 1A) and Env (Figure 3B) upon SR overexpression may very well explain why Gag assembly and virion release are most probably slowed down (Figure 6A). In agreement with this interpretation, the level of packaged genomic RNA into newly formed viral particles was decreased by 65 to 75% (Table 1B). Also in agreement with the above interpretation is the observation that production of high titer lentivectors necessitates expression of the recombinant viral RNA at high levels in vector producing cells .
Despite the low level of incorporated Env (Figure 6), virions produced by cells overexpressing one SR protein retained part of their infectivity on Hela P4 cells. This was not unexpected since only a minimal amount of Env appears to be required to drive infectivity in certain model cell systems .
In summary, the data presented here show that elevated concentrations of SR proteins in HIV-1 expressing cells differentially affected viral RNA and protein expression, resulting in a strong decrease of viral progeny made. Thus one can speculate that the coordinated regulation of HIV-1 splice site utilization by SR proteins is of critical importance to maintain high levels and balanced ratios of the viral RNAs and hence of the viral proteins made in order to direct optimal virus assembly and production. Thus, HIV-1 probably needs to interact with the splicing machinery. In accordance with this view, SC35 is up-regulated and 9G8 down-regulated in HIV-1 infected cells [38, 39]. On a more general basis it has been found that SR proteins influence expression and replication of other viruses such as human papilloma virus type 16  and Adenovirus .
Materials and methods
Plasmids pXJ41-ASF, pXJ42-PR264 and pXJ42-9G8  that respectively encode ASF/SF2, SC35 and 9G8 in eukaryotic cells were provided by J. Stevenin and R. Gattoni (IGBMC Strasbourg, France). The HIV-1 molecular clone is pNL4.3 (GenBank #M19921) .
Cell cultures, transfections and infections
HeLa P4 (provided by P. Charneau) and 293T cells (provided by Genethon) were maintained in Dulbecco's modified Eagle's medium supplemented with 10 % fetal calf serum, 2 mM glutamine and antibiotics (penicillin-streptomycin; Invitrogen). One day before transfection, 3 × 106 293T cells were inoculated in 10-cm Petri dish (except for experiments of Figure 1, see legend). One day later, cells were transfected with 10 μg of proviral pNL4.3 and 4–10 μg of SR-expressing vector or of control plasmid pCLacZ by the calcium phosphate precipitation technique according to manufacturer instructions (Gibco). As observed by immuno-staining and confocal microscopy, more than 70% of the cells were positively transfected. After 12 h, cell culture supernatants were substituted by fresh culture medium. Forty-eight hours after transfection, supernatants were harvested, clarified by filtration through 0.8 μm-pore size filters and ultracentrifuged through a 20 % sucrose cushion. Pelleted viruses were resuspended in TNE buffer (25 mM Tris HCl pH 7.5; 150 mM NaCl; 1 mM EDTA). Virus production was monitored in cell culture supernatants and in virus pellets with a CAp24 ELISA capture assay (kindly provided by Valérie Cheynet and Bernard Mandrand, BioMérieux).
Viral titrations were performed by infection of HeLa P4 cells (1.5 × 105 cells per well of a 24-well plate) with purified viruses containing 1 ng of genomic RNA. After 24 h, cells were fixed and incubated in the presence of X Gal substrate at 37°C until blue color development was complete. Viral titers were determined by counting the number of blue cells in threee different wells.
RNA isolation, Northern blotting and RT-PCR
Transfected cells were harvested 48 h after transfection and washed in phosphate-buffered saline (PBS). Two-third of cells were resuspended in PBS and total cellular RNA was extracted with TRIzol reagent as recommended by the manufacturer (Invitrogen). Culture supernatants were treated as indicated above and the level of CAp24 antigen measured by ELISA. Northern blotting of intracellular viral RNAs was performed with 10 μg of total RNA and slot-blot of virion-associated genomic RNA was performed with 10 ng of CAp24 antigen. After transfer onto a Hybond-N+ membrane (Amersham Pharmacia Biotech), viral RNAs were probed with radiolabeled fragments from Env for Northern blot and from Gag region for slot-blot. All the mRNAs species were quantified by Storm (Amersham).
The splicing products were analyzed by RT-PCR as previously described , except that the forward PCR primer was Odp045 . The PCR products were fractionated on a 6 % acrylamide-7M urea electrophoresis gel and autoradiographed. Individual HIV-1 mRNA species were named according to the nomenclature of Purcell and Martin .
One-third of transfected cells were washed in PBS and lysed in PBS containing 0.5 % Triton. After CAp24 ELISA measurement in cell lysates and in virus pellets, samples were added to 3X gel loading buffer (0.5 M Tris-HCl pH 6.8; 0.8 % SDS; 40 % glycerol; 5 % β-mercaptoethanol; 0.03 % bromophenol blue). For immunoblotting, samples containing equal amounts of CAp24 antigen were loaded on a 10 % SDS-PAGE and fractionated proteins were transferred onto a Hybond P membrane (Amersham Pharmacia Biotech). Viral proteins were probed with monoclonal anti-CAp24 (BioMérieux), polyclonal anti-Vpr (#3951, NIH USA), polyclonal anti-Nef (#331, NIH USA) or monoclonal anti-TMgp41 (Ab 41A9; Hybridolab, Pasteur) antibodies. The bound antibodies were detected with peroxidase-conjugated anti-mouse IgG antibodies and visualized by the SuperSignal West Pico Chemiluminescent Substrate (Pierce).
Immunofluorescence staining and confocal microscopy imaging
Transfected 293 T cells were grown on poly-lysine coated coverglass dishes and fixed 24 h post transfection in 3% paraformaldehyde (diluted in Phosphate Buffer Saline – PBS) for 20 min. The fixative was then removed and the free aldehydes were quenched with 50 mM NH4Cl. Cells were then permeabilized using 0.2 % Triton X-100 for 5 min and blocked in 1% BSA. The fixed cells were incubated for one hour at room temperature with primary antibodies: rabbit anti-MAp17 (NIH, USA), human anti-HIV-1 gp120 Mab(b12) (NIH, USA), rabbit anti-His for His-tagged 9G8 and ASF proteins, and mouse anti-HA1 for HA-tagged SC35 protein (Sigma). The corresponding fluorescent Alexa® 488, 546 and 633-conjugated secondary antibodies were used at 0.5 μg/ml (Molecular probes). Coverslips were washed three times with PBS and mounted on microscope slides with Mowiol (Sigma). Images were acquired on Axioplan 2 Zeiss CLSM 510 confocal microscope with Argon 488/458, HeNe 543, HeNe 633 lasers and plan apochromat 63 × 1.4 oil Ph3 objective, supplied with LSM 510 3.4 software.
Human Immunodeficiency Virus type 1.
viral capsid protein p24.
viral matrix protein p17.
splicing regulatory proteins.
- hnRNP proteins:
heterogenous ribonucleoparticle proteins.
- Site A:
splicing acceptor site. Site D, splicing donor site.
kilobases. WT, wild type.
Phosphate Buffer Saline.
bovine serum albumin.
We are grateful to J. Stevenin and R. Gattoni for their gifts of anti-ASF/SF2, anti-SC35 and anti-9G8 antibodies and for the SR protein expression plasmids, B. Mandrand (CNRS BioMérieux) for anti-CAp24 ELISA and the NIH (USA) for reagents. Work supported by ANRS, Sidaction and the European TRIoH Consortium. SJ was the recipient of an ANRS fellowship.
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