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Journal of Virology, March 2001, p. 2776-2785, Vol. 75, No. 6
0022-538X/01/$04.00+0 DOI: 10.1128/JVI.75.6.2776-2785.2001
Copyright © 2001, American Society for Microbiology. All rights reserved.
Novel, Live Attenuated Simian Immunodeficiency Virus Constructs
Containing Major Deletions in Leader RNA Sequences
Yongjun
Guan,1,2
James B.
Whitney,1,3
Chen
Liang,1,2 and
Mark
A.
Wainberg1,2,3,*
McGill University AIDS Centre, Lady Davis
Institute-Jewish General Hospital, Montreal, Quebec, Canada H3T
1E2,1 and Department of
Medicine2 and Department of Microbiology
and Immunology,3 McGill University,
Montreal, Quebec, Canada H3A 2B4
Received 14 August 2000/Accepted 20 December 2000
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ABSTRACT |
We have constructed a series of simian immunodeficiency virus (SIV)
mutants containing deletions within a 97-nucleotide (nt) region of the
leader sequence. Deletions in this region markedly decreased the
replication capacity in tissue culture, i.e., in both the C8166 and
CEMx174 cell lines, as well as in rhesus macaque peripheral blood
mononuclear cells. In addition, these deletions adversely affected the
packaging of viral genomic RNA into virions, the processing of Gag
precursor proteins, and patterns of viral proteins in virions, as
assessed by biochemical labeling and polyacrylamide gel
electrophoresis. Different levels of attenuation were achieved by
varying the size and position of deletions within this 97-nt region,
and among a series of constructs that were generated, it was possible
to rank in vitro virulence relative to that of wild-type virus. In all
of these cases, the most severe impact on viral replication was
observed when the deletions that were made were located at the 3'
rather than 5' end of the leader region. The potential of viral
reversion over protracted periods was investigated by repeated viral
passage in CEMx174 cells. The results showed that several of these
constructs showed no signs of reversion after more than 6 months in
tissue culture. Thus, a series of novel, attenuated SIV constructs have
been developed that are significantly impaired in replication capacity
yet retain all viral genes. One of these viruses, termed SD4, may be
appropriate for study with rhesus macaques, in order to determine
whether reversions will occur in vivo and to further study this virus as a candidate for attenuated vaccination.
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INTRODUCTION |
Simian immunodeficiency virus (SIV)
is a primate lentivirus closely related to human immunodeficiency virus
type 1 (HIV-1) (14, 21, 35, 38, 41). Highly attenuated
strains of SIV containing deletions in nonessential genes have been
shown to elicit strong protection against pathogenic challenge in
primate models (1, 7, 9, 13, 43). Although live attenuated nef-deleted viruses have protected monkeys against challenge
with wild-type viruses, this type of vaccine is considered unacceptable because of reversions and safety concerns (18, 38). For
example, multiply deleted SIV strains have been shown to be pathogenic in neonatal macaques (2, 3). Notably, as well, these
mutants are able to replicate in permissive cell lines (15,
34). Although the relationship between viral replication
capacity and pathogenesis is not always clear, high plasma viral load
is strongly correlated with disease progression in the case of HIV-1
(33).
Extensive studies have shown that leader sequences within the HIV-1
genome, between the primer binding site and the major splice donor
site, play a critical role in various aspects of viral replication,
including packaging of viral genomic RNA, Gag protein
processing, reverse transcription, and gene expression (20, 22,
24, 26, 28, 29). HIV mutants containing deletions in this region
are highly attenuated in ability to grow in permissive cell lines, yet
retain the ability to synthesize all viral proteins. Recent work has
also revealed a similar role for the leader sequences in SIV
(17).
Deletion of select areas of the leader sequences in HIV and SIV may
conceivably represent a good vaccine strategy. To further study this
topic, we have constructed a series of mutated SIV variants containing
deletions in this region. These mutated SIV strains displayed similar
patterns of impairment in both permissive cell lines and in monkey
peripheral blood mononuclear cells (PBMCs), and certain of these
viruses are stable in tissue culture for periods of 6 months to 1 year,
with no sign that reversions or compensatory mutations have occurred.
Animal trials of these novel, live attenuated viruses will be needed to
delineate relationships between replication capacity and pathogenesis
and to establish potential protective capacity and correlates of immunity.
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MATERIALS AND METHODS |
Construction of deletion mutants.
The full-length infectious
clone of SIV, SIVmac239/WT (17, 23), was used to construct
deletion mutants. We used a PCR-based mutagenesis method to generate
deletions downstream of the primer binding site; Pfu
polymerase was used to increase the fidelity of the PCR. Briefly, the
region between the NarI and BamHI sites in
SIVmac239/WT was replaced with PCR fragments to generate mutant constructs. Figure 1 graphically
illustrates the mutants generated. Primers pSD1a/pSgag1 were used for
the SD1a deletion, and primers pSD1b/pSgag1 and pSD1c/pSgag1 were used
for SD1b and SD1c, respectively. For construction of the SD4, SD5, and
SD6 deletions, PCR fragments (pSD4/pSgag1, pSD5/pSgag1, and pSD6/pSgag1
for SD4, SD5, and SD5, respectively) were purified and were then used
as mega-primers paired with primer pSU5. The resulting PCR fragments
were then used to replace the region between NarI and
BamHI sites in SIVmac239/WT. The construction of the SD,
SD1, SD2, and SD3 mutants has been described previously
(17), and the sequences of novel primers used in the
present work are as follows: pSD1a,
5'-GATTGGCGCCTGAACAGGGAC/GCAGTAAGGGCGGCAGG-3' (+301 to +321/+363 to +379); pSD1b,
5'-GATTGGCGCCTGAACAGGGAC/GG CGGCAGGAACCAACC-3' (+301 to
+321/+371 to +387); pSD1c,
5'-GATTGGCGCCTGAACAGGGAC/AACCAACCACGACGGAG-3' (+301 to
+321/+380 to +396); pSD4,
5'-CTGAGTGAAGGCAGTAAG/GCTCCTATAAAGGCGCGGGC-3' (+353 to
+370/+398 to +418); pSD5,
5'-GCAGTAAGGGCGGCAGG/GCTCCTATAAAGGCGCGGGTC-3' (+363 to
+379/+398 to +418); and pSD6,
5'-CGGCTGAGTGAAGGCAGTAAG/AACCAACCACGACGGAG-3' (+350 to
+370/+380 to +396). Other primers used in this work have been described
previously (17). The validity of all constructs was confirmed by sequencing. Nucleotide designations are based on published
sequences; the transcription initiation site corresponds to position +1
(23).

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FIG. 1.
Illustration of the deletion constructs used in this
study. Secondary structures of the U5-leader stem and the putative DIS
stem-loop of SIVmac239 leader RNA are shown. The positions of deletion
constructs are relative to the transcription initiation site and are
shown next to the RNA structure. These positions are also indicated in
the diagram of secondary structure. Both the primer binding site (PBS)
and the DIS palindrome sequences are highlighted.
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Cells and preparation of virus stocks.
COS-7 cells and 293T
cells were maintained in Dulbecco's modified Eagle's medium (DMEM)
supplemented with 10% heat-inactivated fetal bovine serum. C8166 cells
and CEMx174 cells (39) were maintained in RPMI 1640 medium
supplemented with 10% heat-inactivated fetal bovine serum. Monkey
PBMCs were isolated from the blood of healthy rhesus macaques and
were stimulated with phytohemagglutinin for 3 days and then maintained
in RPMI 1640 medium supplemented with 10% heat-inactivated fetal
bovine serum and 20 U of interleukin 2 per ml. All media and sera were
purchased from GIBCO (Burlington, Ontario, Canada). Molecular
constructs were purified with a Maxi Plasmid kit (Qiagen, Inc.,
Mississauga, Ontario, Canada). Both COS-7 and 293T cells were
transfected with the constructs described above by using
Lipofectamine-Plus reagent (GIBCO). Virus-containing culture fluids
were harvested at 60 h after transfection and were clarified by
centrifugation for 30 min at 4°C at 3,000 rpm in a Beckman GS-6R
centrifuge. Viral stocks were passed through a 0.2-µm-pore-diameter
filter and stored in 0.5- or 1-ml aliquots at
70°C. The
concentration of p27 antigen in these stocks was quantified with a
Coulter SIV core antigen assay kit (Immunotech, Inc., Westbrook, Maine).
Virus replication.
Viral stocks were thawed and treated with
100 U of DNase I in the presence of 10 mM MgCl2
at 37°C for 1 h to eliminate any residual contaminating plasmids
from the transfection. Infection of C8166 cells or CEMx174 cells was
generally performed by incubating 106 cells at
37°C for 2 h with an amount of virus equivalent to 10 ng of p27
antigen (for exceptions, see figure legends). Infected cells were then
washed twice with phosphate-buffered saline and resuspended in fresh
medium. Cells were split at a 1:3 ratio twice per week if they had
grown to a sufficient level; otherwise, the culture fluid was replaced
with fresh medium. Supernatants were monitored for virus production by
reverse transcriptase (RT) assay. Virus infectivity (50% tissue
culture infective dose [TCID50]) was determined
by infection of CEMx174 cells as described previously (11). The sMAGI assay was also performed to determine the
infectivity of mutated and wild-type viruses as described previously
(5).
Virus replication was also performed in primary rhesus monkey
PBMCs. Activated PBMCs (5 × 10
6) were
infected with SIV stocks containing 10 ng of p27 at 37°C
for 2 h
; the cells were then washed extensively to remove
any
remaining virus. Cells were maintained in 10 ml of culture
medium as
described above. Virus production in culture fluids
was monitored by
SIV p27 antigen capture assay by using the Coulter
SIV core antigen
capture
kit.
Analysis of viral proteins by radiolabeling and
immunoprecipitation.
In order to radiolabel viral proteins, 293T
cells were transfected with wild-type or mutant constructs. After
20 h, cells were starved at 37°C for 30 min in DMEM without
methionine or cysteine. Radiolabeling was performed with
[35S]Met and [35S]Cys
at a concentration of 100 µCi/ml for 30 min at 37°C. Then, the
cells were thoroughly washed with complete DMEM and cultured for 1 h. Culture fluids were collected and clarified with a Beckman GS-6R
bench centrifuge at 3,000 rpm for 30 min at 4°C. Viral particles were
further purified through a 20% sucrose cushion at 40,000 rpm for
1 h at 4°C with an SW41 rotor in a Beckman L8-M ultracentrifuge. Virus pellets were suspended in 1× sodium dodecyl
sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) loading buffer
(31), boiled for 5 min, and then fractionated by SDS-PAGE
(12% polyacrylamide) and exposed to X-ray film. The labeled
cells were washed twice with cold phosphate-buffered saline and lysed
in buffer containing 0.1% NP-40. Cell lysates were incubated with a
monoclonal antibody (MAb) directed against SIV p27 at 4°C for 30 min,
and the resultant antigen-antibody complexes were precipitated by a
30-min incubation with protein A-Sepharose CL-4B (Amersham Pharmacia
Biotech, Montreal, Quebec, Canada). Recovered viral proteins
were analyzed by SDS-PAGE (12% polyacrylamide) and exposed to X-ray
film (31).
Packaging of viral genomic RNA.
Viral RNA was
isolated with the QIAamp viral RNA mini kit (Qiagen) from equivalent
amounts of COS-7 cell-derived viral preparations based on levels of SIV
p27 antigen. RNA samples were treated with RNase-free DNase I at 37°C
for 30 min to eliminate possible DNA contamination. DNase I
was then inactivated by incubation at 75°C for 10 min. The viral RNA
samples were quantified by RT-PCR with the Titan One Tube RT-PCR system
(Boehringer Mannheim, Inc., Montreal, Quebec, Canada) as described
previously (17). Relative amounts of products were
quantified by molecular imaging (Bio-Rad, Toronto, Ontario, Canada).
Levels of genomic RNA packaging were calculated on the basis of
four independent experiments, with wild-type viral values arbitrarily
set at 1.0.
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RESULTS |
A short nucleotide sequence downstream of the primer binding site
plays a key role in SIV replication.
We previously constructed
four SIV mutants (SD, SD1, SD2, and SD3) containing large deletions
within a 97-nucleotide (nt) region downstream of the primer binding
site. Each of these deletions resulted in impaired viral
replication in C8166 cells, and yet, in one case, compensatory
mutations and restored viral replication capacity were observed over
time (17). To further investigate the possibility of
establishing attenuated strains that would be more permanently
attenuated and to further assess which sequences were responsible for
impaired virus replication, we generated six additional deletion
constructs (Fig. 1). The original SD1 deletion of 22 nt at positions
+322 to + 344 had little long-term impact on virus replication, so we
extended the deletion to lengths of 41, 49, and 58 nt, i.e., constructs
SD1a (+322 to +362), SD1b (+322 to +370), and SD1c (+322 to +379),
respectively (Fig. 1). RNA secondary structure analysis indicated that
a nucleotide stretch downstream of the primer binding site can form
a stem with an upstream sequence (i.e., the U5-leader stem)
(37). A sequence homology search for a binding site for a
regulatory factor revealed sequences with high homology to the SP1
binding site at positions +370 to +397 in SIV (data not shown).
Accordingly, we generated the deletion mutants, termed SD4 (+371 to
+397), SD5 (+380 to +397), and SD6 (+371 to +379) (Fig. 1) and studied
the effect of these deletions on virus replication. The results in Fig.
2A show that both the SD1a and SD1b
viruses were partially impaired, while each of the SD1c, SD4, SD5, and
SD6 viruses was severely impaired in ability to replicate in C8166
cells. The SD6 construct retains the 5' portion of the exact sequence
that was deleted in SD1c, but not in SD1a or SD1b. These findings
suggest that the deletion of as few as 9 nt at positions +371 to +379
contributed to severely impaired virus replication. The fact that the
extent of impairment of SD5 was similar to that of SD3, SD1c, and SD suggests that the sequences at positions +380 to +397 (i.e., between the U5-leader stem and the DIS stem-loop) are also important in this
regard.

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FIG. 2.
Replication capacity of mutated viruses in C8166 cells.
(A) Equivalent amounts of virus from COS-7-transfected cells were used
to infect C8166 cells based on levels of p27 antigen (10 ng per
106 cells). Viral replication was monitored by RT assay of
culture fluids. Mock transfection denotes exposure of cells to
heat-inactivated wild-type (WT) virus as a negative control. (B)
Replication capacity of mutated viruses during long-term tissue culture
in C8166 cells.
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We have previously shown that long-term culture of cells infected by
the SD2 virus resulted in reversions (
17). However,
maintenance of cells infected by the SD4, SD5, SD6, and SD1c viruses
revealed that the SD4 and SD1c viruses appeared to be stably
impaired
(Fig.
2B). In contrast, the SD5 and SD6 viruses achieved
higher
levels of viral replication after 9 to 10
weeks.
Replication of deleted viruses in CEMx174 cells.
The B/T
hybrid cell line known as CEMx174 lends itself well to the replication
of SIV (39). The results of Fig.
3A show that the SD1 mutants replicated
in these cells with kinetics similar to those of wild-type viruses.
Although both SD1a and SD1b were partially impaired, this occurred to a
lesser degree than in the C8166 cells. SD2, SD5, and SD6 displayed
moderately delayed growth, but still replicated faster in CEMx174 cells
than in the C8166 line. And, as with C8166 cells, the SD, SD3, SD1c,
and SD4 mutants were severely impaired in ability to grow in the
CEMx174 cell line.

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FIG. 3.
Replication capacity of mutated viruses in CEMx174
cells. (A) Equivalent amounts of virus from COS-7-transfected cells
were used to infect CEMx174 cells based on levels of p27 antigen (10 ng
per 106 cells). Viral replication was monitored by RT assay
of culture fluids. Mock infection denotes exposure of cells to
heat-inactivated wild-type (WT) virus as a negative control. (B)
Replication capacity of mutated viruses during long-term tissue
culture.
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The long-term culture of infected CEMx174 cells showed that SD4 viruses
attained peak levels of RT activity at 6 weeks postinfection
(Fig.
3B),
while the SD, SD1c, and SD3 viruses did not show any
signs of reversion
after 6 months. The combined results of infections
in C8166 and CEMx174
cells show that the SD2, SD5, and SD6 viruses
are attenuated to an
extent that is tolerated by both cell lines,
while SD4 is a highly
attenuated virus that can grow marginally
in CEMx174 cells, but not in
C8166
cells.
The potential for viral reversion over protracted periods was also
investigated with CEMx174 cells. Viruses from the peaks
of RT activity
in the initial infection were used to infect fresh
cells. The
replication kinetics of these second-passage viruses
are shown in Fig.
4. All of the passaged viruses still
showed
impaired replication kinetics compared to wild-type virus. The
results of PCR and sequencing confirmed that all of these viruses
retained their original deletions (data not shown).

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FIG. 4.
Replication capacity of mutated virus during the second
passage in CEMx174 cells. CEMx174 cells were infected with equivalent
amounts of virus from the peak time of RT production after initial
infection based on levels of p27 antigen (10 ng per 106
cells). Viral replication was monitored by RT assay of culture
fluids. Mock infection denotes exposure of cells to heat-inactivated
wild-type (WT) virus as a negative control.
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The infectiousness of these mutated viruses was also determined by the
TCID
50 assay in CEMx174 cells and by sMAGI assay
(Fig.
5). The results are consistent with
those obtained by growth curve
assay as described above. Therefore, the
deletion of leader sequences
downstream of the primer binding site
adversely affected viral
infectiousness.

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FIG. 5.
Infectiousness of the wild type (WT) and various mutated
viruses. The results shown are the averages of three independent
experiments. Each of the SD, SD1c, SD3, and SD4 viruses was shown to be
poorly infectious, with RT values being below the threshold sensitivity
of the assay (dashed line). Mock infection represents a negative
control in which cells were exposed to heat-inactivated wild-type
virus. (A) TCID50s of the wild type and various mutated
viruses were determined by infection of CEMx174 cells as described in
Materials and Methods. (B) Infectivity was tested by sMAGI assays as
described previously (5). Numbers of blue-stained cells
were scored and plotted.
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Replication of deleted viruses in macaque PBMCs.
As
shown in Fig. 6A, SD1 viruses
(deletion of the sequence of position +322 to +344) grew in PBMCs
with kinetics close to those of wild-type virus. In contrast, both SD1a
and SD1b showed impairment in replication capacity, growing to only 20 to 40% of wild-type levels. The replication of the SD1c mutant was
completely impaired in these studies. This again reaffirms that the
9-nt sequences at positions +371 to +379 are extremely important. This is also shown in the case of the SD6 virus, which was highly impaired in replication capacity and grew to only 5% of wild-type levels. Deletion of the sequences from +380 to +397 (SD5) only moderately impaired viral replication (i.e., 10% of the wild-type virus level), while SD2 and SD4 were even further diminished in this regard, i.e.,
<1% of wild-type levels. As with SD1c, the replication levels of the
SD and SD3 viruses were below the limit of detection. This is in
contrast to infection in C8166 cells, in which SD and SD3 produced
detectable levels of viral p27 antigen (17).
Therefore, these mutants were also attenuated in monkey PBMCs, in
which the relative in vitro virulence of those viruses can be ranked
as follows: SD, SD3,
SD1c<SD4<SD2<SD6<SD5<SD1b<SD1a<SD1<wild type.

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FIG. 6.
Replication capacity of the wild type (WT) and mutated
viruses in monkey PBMCs. Equivalent amounts of virus were used to
infect rhesus macaque PBMCs based on levels of p27 antigen as
described in Materials and Methods. Viral replication was monitored by
SIV p27 antigen ELISA of culture fluids. Mock infection denotes
exposure of cells to heat-inactivated wild-type virus as a negative
control. The dashed line representing 0.01 ng of p27 per ml
illustrates the threshold sensitivity of the assay. (A) Growth curves
in PBMCs obtained from monkey 1. (B) Growth curves in PBMCs
harvested 6 months later from the same animal. (C) Growth curves
in PBMCs from monkey 2.
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We further examined the relative replication capacity of these mutants
in monkey PBMCs by using blood samples from the same
animal
harvested 6 months apart as well as blood from another
monkey. The
results in Fig.
6B and C show that our mutant viruses
were
similarly impaired in replication capacity, as were the viruses
studied
in Fig.
6A, except that the SD2 virus displayed marginally
greater replication in the PBMCs of monkey 2 than in those of
monkey
1.
To investigate the potential for phenotypic reversion of these mutants
after replication in monkey PBMCs, several cell-free
viruses
harvested at 7 days after infection of PBMCs (Fig.
6A)
were used to
infect new PBMCs from the same animal as well as
CEMx174 cells. As
shown in Fig.
7A and B, these passaged
viruses
still showed impaired replication kinetics similar to those
seen
during the initial infection of the PBMCs (Fig.
6A) and
CEMx174
cells (Fig.
3A).

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FIG. 7.
Replication capacity of mutated virus derived from
monkey PBMCs. Viruses equivalent to 200 pg of p27 antigen derived
from infected PBMCs of monkey 1 were used to infect 105
PBMCs of the same monkey or 105 CEMx174 cells.
Viral replication was monitored by SIV p27 antigen enzyme-linked
immunosorbent assay of culture fluids. Mock infection denotes exposure
of cells to heat-inactivated wild-type (WT) virus as a negative
control. The dashed line representing 0.01 ng of p27 per ml illustrates
the threshold sensitivity of the assay. (A) Growth curves of
second-passage virus in monkey PBMCs. (B) Growth curves of
second-passage virus in CEMx174 cells.
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Deletions of sequences at positions +322 to +418 affect both
packaging of viral genomic RNA and processing of Gag precursor
protein.
We previously showed that a large deletion in each of the
SD, SD2, and SD3 constructs could adversely impact packaging of viral
genomic RNA (17). To study this subject
mechanistically in these and our more stably attenuated viruses, we
next analyzed the efficiency of viral RNA packaging in the mutated
viruses containing small deletions in the leader region. RT-PCR was
employed to amplify a region of the gag gene as previously
described (17). The results in Fig.
8 show that both the SD1a and SD1b
mutants packaged viral RNA with efficiency similar to that of wild-type
virus, while the deletions in the SD1c, SD4, SD5, and SD6 constructs
reduced packaging to 19, 21, 35, and 33% of wild-type levels,
respectively. Thus, the sequences at both positions +371 to +379 and
+380 to +397 apparently play a key role in viral RNA packaging, while those at positions +322 to +370 do not.

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FIG. 8.
Viral RNA packaging in the wild type (WT) and mutated
viruses. Equivalent amounts of virus derived from transfected COS-7
cells, based on levels of p27 antigen, were used to prepare viral RNA,
which was then used as a template for quantitative RT-PCR to detect the
full-length viral RNA genome in an 18-cycle PCR. Relative amounts of a
114-bp DNA product were quantified by molecular imaging, with wild-type
values arbitrarily set at 1.0. Reactions run with RNA template,
digested by DNase-free RNase, served as a negative control for each
sample to exclude any potential DNA contamination. Relative amounts of
viral RNA that were packaged were determined on the basis of four
different experiments.
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To shed further light on these deficits, we also examined the
processing of Gag precursor proteins through short-term radiolabeling
and immunoprecipitation experiments, since previous work with
HIV-1 had
shown that leader sequences are important for protein
processing
(
28,
29). Immunoprecipitation of viral proteins
in cell
lysates was achieved through use of MAbs against SIV p27
(CA); this
permitted identification of the Gag precursor Pr55,
the intermediate
proteins p40 and p28, and the mature p27 product.
The amount of each
protein was quantified by densitometry, and
for each virus, the
percentage of each band relative to total
protein was plotted (Fig.
9). We found that the SD1 mutant
possessed
proportions of these four proteins similar to those of
wild-type
virus, while all of the other mutants displayed an
accumulation
of each of the Pr55, p40, and p28 proteins and diminished
levels
of p27. Both the SD1a and SD1b mutants appeared to suffer only
minor impairment in the processing of Gag precursor proteins,
while
SD1c and SD6 were moderately affected in this regard. In
contrast, the
deletions in SD2, SD3, SD4, SD5, and SD resulted
in severely impaired
processing of Gag precursor proteins.

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FIG. 9.
Processing of SIV Gag precursor proteins. 293T cells
transfected with wild-type (WT) or mutated SIV constructs were
radiolabeled and viral proteins in the cell lysates were then
immunoprecipitated with MAbs against SIV p27 as described in Materials
and Methods. The positions of viral Gag proteins are shown on the right
side of the gel (A). Mo, mock transfection control. The percentage of
each viral protein relative to all viral proteins detected was
calculated with the NIH Image program. The results are illustrated as
well by a bar graph (B) showing the different percentages of each band
associated with each of the constructs studied, as well as by a line
chart (C), showing a steady change in band representation from
wild-type virus to the mutated constructs.
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To further study this topic,
35S-labeled viral
progeny that were released during 1 h from 293T cells were
purified at 24 h after
transfection; their protein band patterns
are shown in Fig.
10.
Seven of the
protein bands were quantified by densitometry, and
for each virus, the
percentage of each band versus all seven proteins
was plotted (Fig.
10). The seven bands include the Gag precursor
Pr55 (band 1), the Gag
intermediate proteins p40 (band 3) and
p28 (band 6), and the mature p27
product (CA, band 7). The other
three bands, with molecular masses of
43 (band 2), 36 (band 4),
and 34 (band 5) kDa, cannot be easily
identified, but most likely
represent proteins that are found to a
limited extent in virions
(e.g., the integrase, the transmembrane
envelope protein, or the
Gag intermediate proteins present in immature
virions). We found
that the SD1 virus displayed a protein pattern
similar to that
of wild-type virus, while all of the other mutated
viruses appeared
to be modified, particularly with regard to bands 2 and 4, which
were represented only to a limited extent.

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FIG. 10.
Protein band patterns in the wild type (WT) and mutated
SIV. 35S-labeled viral progeny that had been released over
1 h from 293T cells were purified at 24 h after transfection;
protein patterns are shown (A). Mo, mock transfection control. Seven of
the protein bands were quantified by densitometry with the NIH Image
program. For each virus, the percentage of each band versus all seven
bands was calculated. The results are illustrated as well by a bar
graph (B) showing the different percentages of each band associated
with each of the constructs studied, as well as by a line chart (C)
showing a steady change in band representation from wild-type virus to
the mutated constructs.
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DISCUSSION |
The RNA genomes of both HIV-1 and SIV contain a long 5'
untranslated leader sequence that is crucial for viral replication. Although the 5' untranslated leader sequence of SIV has little sequence
homology with that of HIV-1, similar secondary structures have
been predicted for both (37). Studies with HIV-1 have
shown that the leader sequences between the primer binding site and the
major splice donor site are important for viral replication and are
involved in packaging of viral RNA, gene expression, the processing of
viral core protein, and reverse transcription (20, 22,
24-29). In the case of SIV, this region is also involved in the
packaging of viral RNA (17). The present work extends these observations by showing that deletion of the upper part of the
U5-leader stem did not impair viral RNA packaging (SD1a, SD1b), but did
affect both the patterns of viral proteins and Gag precursor processing.
The lower part of the stem-loop is even more important, since all
deletions in this region resulted in severely impaired
replication capacity, as well as decreased packaging of
viral RNA, delayed processing of Gag precursor proteins, and
changed patterns of viral proteins. It may be that a stable
U5-leader stem is essential for virus replication and that this stem is
destroyed by deletions in its lower part, but not upper part. Our
results also show that the sequence between the U5-leader stem-loop and
the putative DIS stem-loop is important. Deletion of this region
adversely affected packaging of viral RNA, processing of Gag proteins,
and patterns of viral proteins. From a mechanistic standpoint, it is
known that viral RNA packaging is a process involving specific recognition between viral proteins and viral RNA elements.
Studies with HIV-1 have shown that the viral nucleocapsid (NC) protein,
which is required for packaging of viral RNA, can bind to viral leader
RNA sequences with high affinity in cell-free assays (8).
An encapsidation signal, located at the 5' end of the viral genome,
consists of four RNA stem-loop structures, termed SL1 to SL4, and of
these, SL1 and SL3 are the major elements that bind NC proteins
(6, 19, 32). Deletions of SL1 in HIV-1 were shown to
impair viral replication, as well as cause delayed processing of Gag
proteins and decreased levels of viral RNA packaging (26,
28). Compensatory point mutations in four distant Gag proteins,
i.e., NC, MA, CA, and p2, were able to restore these deficits
(27, 29). Similar studies with SIV have also shown that
deletions of leader sequences that affect viral RNA packaging can be
rescued by compensatory point mutations in Gag proteins
(17). These observations and the present work suggest the
likelihood of important functional interactions between Gag proteins
and leader sequences in both HIV-1 and SIV. Both the processing of Gag
proteins and encapsidation of viral RNA may require that leader RNA
sequences exist within constraints of proper tertiary structure, which
are highly conserved in both HIV-1 and SIV (37). The
changes reported here with regard to patterns of viral proteins may be
the consequence of impaired processing of Gag proteins. Such delayed
processing, caused by our deletions, may result in abnormal
incorporation of proteins into virions, although other mechanisms to
explain the attenuation effects seen here are also possible and are
under investigation.
The development of a safe, effective vaccine to protect against
infection by HIV-1 must be regarded as a top priority in public health.
In monkeys, live attenuated SIVs have been shown to induce a protective
immune response against pathogenic strains (1, 7, 9, 13,
43). Most of this work has involved deletions of accessory
genes, such as nef, vpr, or vpx.
However, these mutated viruses have retained replication capacity
similar to that of wild-type virus in permissive cell lines (15,
34). In addition, multiply deleted SIV variants have been shown
to be pathogenic in neonatal macaques (2, 3).
In contrast, our group has studied viruses containing deletions in the
noncoding leader regions of both HIV-1 and SIV (17, 25-29). Unlike the SIV strains that have been mutated in
accessory genes, our deleted viruses are significantly impaired in
replication capacity in cell lines, yet they retain all viral genes,
including accessory genes. This may be important, since the Nef protein and other viral nonstructural proteins are important targets of antiviral immune responses (42, 45). In the present work, we have constructed a series of SIV mutants that are attenuated to
different extents in replication capacity in both human T-cell lines
and macaque PBMCs. Next, we wish to evaluate the safety and
protective capacity of these constructs in a macaque monkey model.
The attenuation strategies employed in our work versus deletions in
accessory genes also have different mechanistic consequences. Deletion
of accessory genes can compromise the ability of the virus to replicate
under certain circumstances (10), but such attenuation is
relatively inefficient, since the viruses retain replication
capacity in cell lines and because multiply deleted SIV mutants are
still pathogenic (2, 3, 37). Of course, further deletions
in genes such as tat and rev, which are important for disease progression (42, 44, 45), may have yielded
better long-term results. In contrast, our deletions of leader
sequences may impair multiple steps in the viral life cycle, since the
deleted sequences are contained in all viral RNA species (both
full-length viral RNA and spliced viral RNA) and are involved in
multiple functions (17, 20, 22, 24-29).
Studies of SIV infection of rhesus macaques have indicated that the
intrinsic susceptibility of monkey PBMCs to infection with SIV in
vitro was predictive of relative viremia after SIV challenge (16,
30, 40). However, significant animal-to-animal variation exists,
and it is difficult to identify viruses that fit the "window"
between levels of replication that elicit a protective immune response
and those that result in disease (38). Our panel of novel
mutants displayed a wide range of replication levels, i.e., from minor
to severe impairment, in both T-cell lines and monkey PBMCs. This
constitutes a major advantage of our novel, live attenuated viruses
compared with multi-gene-deleted SIVs that retain high levels of
replication competence in T-cell lines and often in PBMCs as well
(15, 34). In vivo analysis of our panel of mutants may
identify viruses that do fit the "window" required for
identification of the requisite level of viral replication in outbred hosts.
A major safety concern with regard to live attenuated viruses as
vaccine candidates is the problem of phenotypic reversion. Our
experiments with PBMCs from two different monkeys as well as
separate time points showed that our mutants were stably attenuated in
these cells. In contrast, some of our constructs did show a potential
for reversion in a T-cell line; however, such reversion appeared only
gradually and involved several additional mutations (17).
Replication studies with PBMCs showed no reversion of viruses that
had been passaged in either PBMCs or CEMx174 cells. Hence, we hope
that the potential for reversion in vivo, under the pressure of an
immune response, would be minimal and that it might not result in disease.
Of all of the attenuated constructs that we have developed, we believe
that SD4 holds the most potential for work in animals. Further studies
will hopefully be directed toward assessing its stability and ability
to induce immune responsiveness in both newborn and adult rhesus macaques.
 |
ACKNOWLEDGMENTS |
This research was supported by grant RO1 AI43878-01 to M.A.W.
from the National Institute of Allergy and Infectious Diseases, National Institutes of Health. The following reagents
were obtained through the AIDS Research and Reference Reagent
Program, Division of AIDS, NIAID, NIH: the CEMx174 cell line from
Peter Cresswell and the sMAGI assay system from Julie Overbaugh.
We thank Mervi Detorio and Maureen Oliveira for technical assistance.
 |
FOOTNOTES |
*
Corresponding author. Mailing address: McGill
University AIDS Centre, Lady Davis Institute-Jewish General Hospital,
3755 Cote Ste-Catherine Rd., Montreal, Québec, Canada H3T 1E2.
Phone: (514) 340-8260. Fax: (514) 340-7537. E-mail:
mwainb1{at}po-box.mcgill.ca.
 |
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Journal of Virology, March 2001, p. 2776-2785, Vol. 75, No. 6
0022-538X/01/$04.00+0 DOI: 10.1128/JVI.75.6.2776-2785.2001
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