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Journal of Virology, January 2001, p. 242-250, Vol. 75, No. 1
0022-538X/01/$04.00+0 DOI: 10.1128/JVI.75.1.242-250.2001
Copyright © 2001, American Society for Microbiology. All rights reserved.
Viral DNA Synthesis Defects in Assembly-Competent
Rous Sarcoma Virus CA Mutants
Tina M.
Cairns and
Rebecca C.
Craven*
Department of Microbiology and Immunology,
The Pennsylvania State University College of Medicine, Milton S. Hershey Medical Center, Hershey, Pennsylvania 17033
Received 13 June 2000/Accepted 27 September 2000
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ABSTRACT |
The major structural protein of the retroviral core (CA) contains a
conserved sequence motif shared with the CA-like proteins of distantly
related transposable elements. The function of this major region of
homology (MHR) has not been defined, in part due to the baffling array
of phenotypes in mutants of several viruses and the yeast TY3. This
report describes new mutations in the CA protein of Rous sarcoma virus
(RSV) that were designed to test whether these different phenotypes
might indicate distinct functional subdomains in the MHR. A comparison
of 25 substitutions at 10 positions in the RSV conserved motif argues
against this possibility. Most of the replacements destroyed virus
infectivity, although either of two lethal phenotypes was obtained
depending on the residue introduced. At most of the positions, one or
more replacements (generally the more conservative substitutions)
caused a severe replication defect without having any obvious effects
on virus assembly, budding, Gag-Pol and genome incorporation, or
protein processing. The mutant particles exhibited a defect in
endogenous viral DNA synthesis and showed increased sensitivity of the
core proteins to detergent, indicating that the mutations interfere with the formation and/or activity of the virion core. The distribution of these mutations across the MHR, with no evidence of clustering, suggests that the entire region is important for a critical postbudding function. In contrast, a second class of lethal substitutions (those
that destroyed virus assembly and release) consists of alterations that
are expected to cause severe effects on protein structure by disruption
either of the hydrophobic core of the CA carboxyl-terminal domain or of
the hydrogen bond network that stabilizes the domain. We suggest that
this duality of phenotypes is consistent with a role for the MHR in the
maturation process that links the two parts of the life cycle.
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INTRODUCTION |
CA is the major structural component
of retroviruses, forming a protein shell that encases the
ribonucleoprotein complex in the virion core. The ribonucleoprotein
complex is in turn composed of viral RNA (vRNA), tRNA, and the
associated nucleocapsid (NC), reverse transcriptase (RT), and integrase
(IN) proteins in an enzymatic complex that is capable of vDNA synthesis
(4, 14, 41). Structural and sequence similarities have
been noted among CA proteins of retroviruses and CA-like proteins of
other reverse-transcribing elements (20, 21, 25, 27, 34,
47). The most highly conserved region of CA is a motif of about
20 amino acids that lies within the carboxy-terminal domain of the
protein (termed the major homology region [MHR]). The MHR has been
identified in all retroviruses with the exception of spumaretroviruses
(12). Related sequences are present in hepatitis B virus
(47), the retrotransposon Ty3 of Saccharomyces
cerevisiae (32, 36), and certain non-long terminal
repeat (LTR) transposable elements (33), suggesting that
the motif is very probably involved in an aspect of replication common
to all these reverse-transcribing elements. Nevertheless, the functions
in the viral replication cycle of the MHR domain and of CA itself
remain unknown.
The CA protein influences both viral assembly and postassembly
replication activities. CA exists first as a domain of the Gag
precursor, the protein that directs virus assembly and budding, and is
released as a mature structural protein by the action of the viral
protease during subsequent maturation. In Rous sarcoma virus (RSV), the
CA sequence within Gag is not essential for the budding process, since
none of the numerous deletions that span the CA region interfere with
the formation of budding-competent particles in a Gag expression system
(13, 29). However, CA clearly determines the internal
organization of the assembled and budded material, as indicated by the
effects of deletions on particle size (29) and core
integrity (11, 12; N. K. Krishna, T. M. Cairns, and R. C. Craven, unpublished data).
The strongest case for the involvement of CA in postentry replication
events comes from experiments with murine leukemia virus (MuLV).
Certain mutations in the CA domain of MuLV Gag cripple the ability of
the virus to synthesize vDNA upon entry (1). The CA
protein is the target of a restriction event mediated by the
Fv-1 gene product in the target cell that results in a block to replication prior to viral integration (3, 5, 15, 26, 38). Furthermore, MuLV CA has been found in association with core-derived complexes that are in the process of DNA synthesis in the
cytosol of the newly infected cell (18) and with complexes containing completed and integration-competent vDNA molecules (6). A number of mutations in HIV-1 CA also interfere with DNA synthesis in the cell (8).
In hopes of better defining the function of the CA protein, the MHR has
been targeted by mutagenesis in several retroviruses and the yeast Ty3
element. The result has been a perplexing array of phenotypes. In Ty3,
human immunodeficiency virus type 1 (HIV-1), RSV, MuLV, Mason-Pfizer
monkey virus (M-PMV), and bovine leukemia virus, many substitutions
completely abolish particle assembly or cause the release of particles
of aberrant morphology (1, 12, 31, 36, 40, 44). Also,
certain mutations that alter or delete the MHR sequence of HIV-1 Gag
have been reported to cause defects in Gag-membrane binding
(17) and in Gag-Pol packaging into particles (24,
39). A number of additional MHR mutations have been described in
RSV, MuLV, HIV-1, M-PMV, and bovine leukemia virus that have no
discernible defect in assembly yet cause a severe loss of infectivity
(1, 12, 31, 40, 44). Likewise, certain Ty3 mutations also
result in the formation of particles that have severe defects in
reverse transcription and transposition (36). The
existence of this latter class of mutants (those with apparently normal
assembly) argues strongly that the MHR motif influences one or more
events of replication that are distinct from the assembly of
budding-competent particles.
The principal goal of the work presented below was to define the reason
for the failure of such RSV mutants to establish persistent infections.
The mutations present in the five assembly-competent lethal MHR mutants
previously described (12) all mapped to the second half of
the motif, raising the possibility that the two structural elements
within the MHR (a strand-loop element followed by an
-helix)
recently defined in the CA proteins of RSV, HIV, equine infectious
anemia virus, and human T-cell leukemia virus (9, 20, 25,
27) might possess distinguishable functions. The study of new
mutations presented here supports the contrary conclusion. Mutations
whose lethal phenotype cannot be explained by effects on particle
assembly and release map to numerous locations throughout the MHR. In
all cases, the lethality is due to a failure to accomplish a very early
stage of reverse transcription, suggesting that the mutations interfere
with either the formation or the activity of the reverse transcription
complex in the viral core.
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MATERIALS AND METHODS |
Plasmid DNAs and cell lines.
The infectious RSV genome,
carried in plasmid pRC.V8, was derived from pBH.RCAN.HiSV
(16) by replacement of the Schmidt-Ruppin A gag
gene with that of the Prague C strain (12). The viral mutants F167Y, L171I, and R170Q were previously described
(12). New substitutions (see Fig. 1) were created by
oligonucleotide-directed mutagenesis as described previously
(45) with the following primers (nucleotide changes are
underlined): D155N (GGCGCACAT), D155Y
(GGCGAACAT), I156V
(GGACGTGATGC), Q158E
(CATGGAAGGAC), Q158N (CATGAACGGAC), E162D
(CTGATTCCT), E162Q
(ATCTCAATCCT), F164L
(GTCCCTTGT), F164V (GTCCGTTGT),
F164Y (TCCTACGTTG), and L171A
(TCGGGCTATA). Cell lines stably expressing the
F167Y, L171A, L171I and R170Q mutant genomes were created by calcium
phosphate transfection of QT6 cells (35) with mutant
proviral DNAs and selection of hygromycin-resistant colonies. Colonies
were screened for virus production by Western blotting for RSV
antigens. Released particles were analyzed for normal patterns of Gag
cleavage products, envelope glycoproteins, and RT activity on an
exogenous template. The phenotypes of the released particles remained
stable over at least 2 to 3 months of culturing of the cell lines.
Particle release and infectivity.
The expression of Gag
protein from the mutant proviral vectors and the ability of the mutant
proteins to assemble and release virus-like particles were evaluated by
transfection of QT6 cells followed by radiolabeling and
immunoprecipitation as described previously by our laboratory (2,
12, 29, 45). To determine the efficiency of release, QT6 cells
were transfected in duplicate and 24 h later were radiolabeled
with L-[35S]methionine (50 µCi, 1,000 Ci/mmol) using two different methods. The cells of one plate were lysed
after only 5 min to evaluate the levels of Gag expression; from the
second plate, extracellular particles were collected after 3 h of
labeling. The Gag and CA proteins were subsequently immunoprecipitated
with an anti-RSV serum and analyzed by sodium dodecyl
sulfate-polyacrylamide gel electrophoresis and phosphorimaging. A ratio
of the CA released into the medium to the Gag expression level in the
lysates was obtained as an estimate of budding efficiency.
Infections of QT6 cells were initiated by transfection of duplicate
plates with proviral DNAs (12). One set of plates was used
to confirm Gag expression by radioimmunoprecipitation with an anti-RSV
serum 24 h later. The second set was passaged over a period of 30 days, at which point the mutants that continued to produce
extracellular particles (detected by the accumulation of RT activity
and Gag antigens in the medium) were scored as infectious.
Detection of viral DNA in cell lysates.
QT6 cells were
infected with particle suspensions produced from stable cell lines,
concentrated 50-fold using a Centriprep-50 spin column (Amicon), and
standardized by an exogenous RT assay (10). After 18 h, low-molecular-weight viral DNA was isolated from the cells
(23) and used as a template in the Taq PCR with primers derived from the RSV LTR and the 5' and 3' untranslated regions: primer 3 (CTTCATGCAGGTGCTCGTAGTCG) and primer 5 (GCCATTTTACCATTCACCACA) for minus-strand strong stop DNA;
primer 3 and primer 8 (GGATTGGACGAACCACTGAA) for first
strand switch; primer 7 (CAACGACTCTCTGAGTTCTC) and primer 5 for second-strand switch; and primer 8 and primer 9 (CAGGAGTATTGCATAAGACTAC) for 2LTR circles. Additional
primers (TTTTAACCTAACTCCCCTACTTA and
GCCTGAAGCTAGTCACGGAAT) were used to amplify quail
mitochondrial DNA. Each primer pair was tested with plasmid DNA over a
range of annealing temperatures, MgCl2 concentrations, and
DNA concentrations to ensure high sensitivity (
10 copies of DNA) and
responsiveness of the PCR signal to template dilution. One primer of
each pair was end labeled with [
-33P]ATP using T4
polynucleotide kinase and included with template DNA in a 100-µl
reaction mixture containing 2.5 U of Taq polymerase, 200 µM each deoxynucleoside triphosphate, and 15 mM MgCl2.
Standard cycle parameters and product analysis were described
previously (37).
Endogenous reverse transcription.
Particles produced from
cell lines were prepared as described above. Particles produced by
transfection were pelleted through 25% sucrose (400 µl) in a
TLA100.4 rotor at 126,000 × g for 40 min, resuspended
in 200 µl of Tris-buffered saline containing 10 mM MgCl2,
and incubated with 600 U of DNase I for 1 h at 37°C. Destruction
of the plasmid DNA was confirmed by PCR amplification of the
ampicillinase gene in the vector. Virions were incubated in an
endogenous RT reaction buffer (37) with 125 µg of
melittin per ml for 3 h at 42°C, and then viral DNA was
extracted and analyzed by PCR as above.
Detergent treatment of viral particles.
Resistance of the CA
protein to extraction with 1% Triton X-100 was evaluated as previously
described (12), using a rabbit anti-CA serum to detect
radiolabeled protein in supernatant and pellet fractions. The RT
protein was analyzed similarly, except that
4 × 106
transfected QT6 cells were labeled with
L-[35S]methionine (250 µCi, >1,000
Ci/mmol) for 24 h, after which the particles in the medium were
treated with detergent and centrifuged through a 25% sucrose cushion.
Labeled RT
, RT
, and IN proteins in the pellet and supernatant
fractions were analyzed by immunoprecipitation with a goat anti-RT
(
/
) antibody (no. 765-168; National Institutes of Health).
 |
RESULTS |
In our previous study of RSV, all point mutations that allowed the
release of noninfectious particles mapped within second half of the MHR
(specifically, F167Y, L171I, L171V, and R170Q) whereas the mutations
that blocked assembly were scattered throughout the MHR (Fig.
1) (12). This uneven
distribution may simply reflect the limited number of mutations tested
or, alternatively, could be indicative of different functional roles
for the two halves of the domain. Therefore, before focusing on the
reasons for the replication defect in the assembly-competent lethal
mutants, we created several additional mutations targeted primarily at
the conserved sites in the first half of the RSV MHR domain.

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FIG. 1.
Amino acid substitutions in the major homology region of
the RSV Gag protein. The Gag protein is shown with CA shaded and the
MHR in black. The wild-type MHR sequence is positioned below Gag, with
the most highly conserved amino acids underlined and numbered according
to their position in CA. Amino acid substitutions listed below the MHR
are grouped by phenotype. Substitutions resulting in >50% budding
efficiency were scored as budding positive. New substitutions created
in this study are in bold type; the others were previously described
(12).
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Substitutions in the MHR strand-loop subdomain.
A total of 11 new substitutions were created (Fig. 1), including substitutions at
three conserved positions in the strand-loop (I156, Q158, and E162) and
at the nonconserved D155, which lies at the boundary of the conserved
motif and the upstream interdomain linker (9). Additional
substitutions were also constructed at the first amino acid (F164) of
the helical subdomain. The L171A mutation was created for a separate
study but is included in many of the experiments presented below.
All of the new mutant genomes were capable of expressing Gag protein,
detected by radioimmunoprecipitation with an anti-RSV antibody as
described in previous studies (2, 12, 29, 45). The protein
profiles of a representative set of mutants are shown in Fig.
2A. In a quantitative experiment (Fig.
2B), the particle release ability of each mutant (a ratio of particle
release to Gag expression as described in Materials and Methods) was
compared with that of the wild-type parent. The mutants could be
separated easily into two groups. The D155N, I156V, E162D, and L171A
mutants released particles at levels equal to or greater than those of the wild-type parent, and the D155Y mutant averaged 86% of the wild-type level. The E162Q mutant was slightly less efficient, showing
release levels ranging from 50 to 100% with an average of 70% (Fig.
2). In each case, the particles that were released contained properly
processed CA protein (Fig. 2A); no uncleaved Gag precursor or unusual
cleavage intermediates were present in the particles. In contrast, the
remaining mutants showed clear defects in particle release, with
budding efficiencies of <32% of the wild-type level (Q158N, 9%;
Q158E, 11%; F164Y, 27%; and F164L, 32%) (Fig. 2B).

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FIG. 2.
Evaluation of mutant particle release in QT6 cells. (A)
Virions released into the media were visualized by
radioimmunoprecipitation. (B) Budding efficiencies were calculated as a
ratio of the amount of Gag produced to the CA released into the medium,
as discussed in Materials and Methods. All numbers were normalized to
the wild-type value (WT), which was set at 1.00 efficiency. Average
budding efficiencies (center box) and standard deviations (lines) are
shown. uninf'd, uninfected.
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The potential for infectivity was analyzed for each of the new mutants
by monitoring the appearance of RT activity in the medium after
transfection of QT6 cells with proviral plasmid DNA. Not surprisingly,
all four of the budding-defective mutants were completely noninfectious
in this assay, as illustrated by Q158E, Q158N, and F164Y (Fig.
3A). Two of the particle-producing
mutants (D155N and I56V) were indistinguishable from the wild-type
parent in their ability to establish infection following transfection (Fig. 3B). A third mutant (E162D) was invariably successful in establishing infection (Fig. 3A); however, the appearance of RT in the
medium during the 4-week assay period was slower than seen with the
wild-type parent or the other two infectious mutants. Whether genetic
reversion or second-site suppressor mutations occurred during this lag
time has not yet been determined but seems likely, given that the
glutamic acid at position 162 is absolutely conserved in all 20 retroviruses compared in an earlier study (12).
Interestingly, three more recently described fish retroviruses lack
this glutamic acid (30).

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FIG. 3.
Establishment of infection followed by monitoring RT
activity in the media of transfected QT6 cells. (A and B) Medium
samples were collected at intervals over a span of 1 month following
transfection. Viruses with RT activity at background (i.e., equal to
the untransfected) levels after this period were scored as
noninfectious. untr'f, untransfected.
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Most important for the remainder of this study is a group of four
mutants (D155Y, E162Q, F164V, and L171A) which failed to infect (Fig.
3), even though their ability to assemble and release virus particles
was near normal. These new mutants join four mutants with a similar
phenotype (F167Y, R170Q, L171I, and L171V), which were described in our
earlier study (12). Quite striking is the fact that the
combined members of this mutant class map across the MHR sequence with
no obvious clustering (Fig. 1). The substitutions that cause the
assembly-defective phenotype are similarly distributed. Only at one
position (Q158) did every substitution destroy assembly. This greater
sensitivity may be indicative of the unusual role of the conserved
glutamine in the CA structure (see Discussion). Other than this, there
is no evidence that the two structural elements that compose the MHR
(the strand-loop and
-helical elements) are functionally distinct.
Detection of viral DNA in infected cells.
Having obtained a
sizeable collection of mutations that destroyed infectivity but not
particle assembly, we investigated the reasons for this replication
defect. The L171I mutant, which has been the most carefully
characterized RSV mutant, served as the focus of the experiments below.
Additional mutants with substitutions in the loop (D155Y and E162Q) and
in the
-helical subdomain (F167Y, L171A, and R170Q) were included in
most experiments as well.
Initially, low-molecular-weight DNA extracted from QT6 cells infected
with the mutant viruses for 18 h was analyzed for full-length viral DNA by Southern blotting and by PCR amplification of the 2LTR
circle junction DNA (formed in the cell as a result of circularization of full-length linear viral DNA). In both tests, no completed viral DNA
molecules could be detected in samples from cells infected with the
L171A, L171I, and F167Y mutants (data not shown). The R170Q, D155Y, and
E162Q mutants also failed to produce detectable 2LTR DNA in infected
cells (data not shown).
The DNA samples were next analyzed for the presence of incomplete DNA
products by using PCR primer pairs that amplify viral DNAs containing
the minus-strand strong-stop sequence (the first 101 bases) and
molecules whose synthesis proceeded at least through the point of the
first strand switch (169 bases) or the second strand switch (586 bases). All three viral DNA sequences were easily detected in samples
from cells infected with wild-type virus (Fig.
4A), whereas little or no viral DNA could
be detected in samples from mutant-infected cells. Quail mitochondrial
DNA was present in all samples, however, confirming the consistent performance of the DNA extraction and PCR steps. To estimate the degree
of the defect, template DNAs were serially diluted prior to
amplification (Fig. 4B). The level of strong-stop DNA in L171A-infected cells proved to be reduced >1,000-fold compared to that in
wild-type-infected cells. The F167Y and L171I mutations caused a
reduction of 100-fold. Finally, detection of viral DNA was no better
when the infected cells were lysed and DNA was extracted at earlier
times after infection (2 to 8 h postinfection [data not shown]),
giving no indication that the viral DNA was synthesized and then
degraded. Thus, it appears that even at the earliest stages of
infection tested (synthesis of the first 101 nucleotides of DNA), these mutants are severely deficient in viral DNA synthesis.

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FIG. 4.
Viral DNAs in infected QT6 cells. Cells were infected
with RSV particles collected from stable cell lines.
Low-molecular-weight DNA was extracted and analyzed by amplification
using the LTR primers described in Materials and Methods and with the
quail mitochondrial DNA primers. (A) Viral DNA detected in lysates of
cells infected for 18 h. (B) Template DNAs analyzed in panel A
were diluted prior to amplification in order to compare the relative
amounts of minus-strand strong-stop DNA in cells infected with
wild-type (WT) and MHR mutant virus. uninf'd, uninfected; mito, quail
mitochondrial DNA.
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Endogenous reverse transcription.
The next step was to
determine whether the defect that caused the severe loss of DNA
synthesis in infected cells was also evident in extracellular
particles. Although our earlier report showed the presence of some
endogenous reverse transcription ability in mutant particles isolated
from cell lines (12), this was reevaluated by applying the
more quantitative PCR-based assay to the broader set of mutants now
available. Minus-strand strong-stop DNA was clearly detectable in all
samples (Fig. 5A), as previously reported
(12). However, dilution of the template DNA showed that
the level of viral DNA in the mutant particles was actually lower than
that in wild-type particles by a factor ranging from 10-fold (D155Y,
E162Q, and F167Y) to as much as 100-fold (L171A and L171I). The
infectious mutant D155N was indistinguishable from the wild-type parent
in the endogenous reverse transcription assay.

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FIG. 5.
Efficiency of reverse transcription of the endogenous
viral RNA. Particles were collected from stable cell lines (wild type
[WT], F167Y, L171A, and L171I) or from transfected cells (WT, D155N,
D155Y, and E162Q), permeabilized with melittin, and incubated with
dNTPs for three hours at 42°C. The resulting DNA was extracted,
diluted, and amplified as before. The relative amounts of minus-strand
strong stop (A) or first strand switch (B) DNA products in wild-type
and MHR mutant virions were compared. F167Y particles collected from
transfected cells showed the same 10-fold deficit in endogenous reverse
transcription activity as those collected from the stable cell line
(data not shown).
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The failure of the previous study (12) to find this defect
in the F167Y, R170Q, and L171I mutant particles was probably due to the
use of a crude and nonquantitative assay method that was dependent on
observation of the strong-stop DNA band among a smear of DNA products
on a sequencing gel. It is also likely that the batch-selected cultures
used to produce the R170Q and F167Y mutant particles may have contained
revertant viruses (J. B. Bowzard, unpublished data). In the
present study, the use of the more quantitative and highly reproducible
PCR-based method allowed the detection of a DNA synthesis defect in
each of the assembly-competent but noninfectious mutants, regardless of
whether the particles were produced by cloned cell lines (F167Y, L171I, and L171A) or by transfection (F167Y, E162Q, and D155Y).
The presence of more extended DNA products was also evaluated in the
endogenous reverse transcription reactions. The noninfectious mutants
were deficient in the synthesis of the first strand-switch product, but
with the exception of the L171A mutant, the defect appeared no more
severe than at the strong-stop stage (Fig. 5B); in other words, the
response to template dilution was identical with the two sets of
primers. Finally, the sensitivity of detection of the second
strand-switch product was too low even in the wild-type samples to
allow a quantitative comparison with the strong-stop and first strand-
switch products.
RT content.
The major defect at an early stage of the
endogenous reverse transcriptase reaction implies that something is
very wrong with the protein-RNA complex that makes up the reverse
transcription machinery. For this reason, the mutant viruses were
examined for abnormalities that might explain the defect in viral DNA synthesis.
The mutant particles were not deficient in enzymatically active RT. The
CA protein in mutant and wild-type particles was evaluated by Western
blotting of particle suspensions that had been standardized for their
RT content by using an exogenous poly(A) template and an oligo(dT)
primer (Fig. 6). No variation in the
enzyme activity-to-CA ratio that could explain the DNA synthesis defect
was found in any of the mutants. Furthermore, L171I mutant particles
contain normal ratios of RT
, RT
, and IN protein (see below), as
do the F167Y, R170Q, and L171A mutants (data not shown). Thus, the
failure of mutants to synthesize DNA is not explained by defects in the packaging or processing of the Gag-Pol precursor protein.

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FIG. 6.
The ratio of CA to RT per particle is equivalent between
wild-type and mutant viruses. Particles were normalized by RT activity
on an exogenous template/primer, serially diluted, and separated by
SDS-PAGE. Viral proteins were transferred to nitrocellulose by Western
blotting and incubated with anti-RSV serum. The relative amount of CA
protein per sample was examined. untr'f, untransfected.
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Viral RNA content.
Although the F167Y and L171I particles were
shown previously by slot blot analysis to contain viral RNA
(12), the failure of DNA synthesis raised the possibility
that viral RNA might be degraded inside the particle. Therefore, the
viral RNA was extracted and analyzed by standard methods (19,
37) (Fig. 7). Genomic RNA from the
D155Y, E162Q, F167Y, L171A, L171I, and R170Q mutants proved to be
intact and was present primarily in the form of dimers (Fig. 7A), as
was that from the mutant F164V (data not shown). No degradation of the
viral RNA template and no deficit in the amount recovered were detected
in any case. The thermostability of the dimeric RNAs of the L171I
mutant was tested by exposing the nucleic acid to temperatures as high
as 65°C prior to electrophoresis. The mutant RNA showed the same
melting profile as that from wild-type particles (Fig. 7B); the same
result was obtained with F167Y and L171A particles as well (data not
shown). Thus, we detected no gross distortion of the viral genomic RNA
that could explain the defect in reverse transcription.

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FIG. 7.
Analysis of viral RNA in wild-type and mutant particles.
(A) Nondenaturing Northern blot analysis of RNA extracted from
particles. (B) RNA melting profiles were generated by incubating the
viral RNAs at the indicated temperatures for 10 min prior to loading on
a nondenaturing agarose gel. WT, wild type; D, dimer; M, monomer.
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Association of CA and RT with detergent-resistant core
material.
A number of laboratories have isolated material derived
from the RSV core, including CA, by centrifugation of detergent-treated virions through sucrose (4, 12, 41). In our laboratory, such a method has allowed the reproducible recovery of approximately 25 to 30% of the total CA protein in particulate form from infectious wild-type virions (12) (Fig.
8A). However, with the F164V or F167Y
mutants, the amount of CA protein recovered in the detergent-resistant pellet was greatly reduced, ranging between 0 and 3% of the total amount of CA (Fig. 8A). This was similar to our previous findings with
the L171I mutant (12). For the D155Y and E162Q mutants, a
somewhat less severe defect was seen; approximately 10% of CA was
recovered in the pellet, still reproducibly lower than the 30%
recovered from the wild-type particles.

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FIG. 8.
CA and RT are displaced from detergent-resistant
complexes by mutations in the MHR. Particles produced by transfection
were incubated with or without detergent prior to ultracentrifugation
through a sucrose cushion. Pellet and supernatant fractions were
collected and immunoprecipitated with a monoclonal antibody against CA
(A) or RT (B). A background band recovered by the RT
immunoprecipitation migrated slightly above the IN protein and appeared
in both infected and uninfected controls. WT, wild type; TX-100, Triton
X-100; P, pellet; S, supernatant.
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The distribution of RT between the particulate and pellet fractions was
also altered by the L171I mutation. For wild-type particles,
approximately 30% of RT
and 40% of RT
remained with the pellet
after detergent treatment (Fig. 8B). In contrast, detergent treatment
of the L171I mutant particles solubilized all the detectable RT
and
left only a trace amount of RT
(4 to 6%, as quantitated by
phosphorimaging analysis of the results of two independent experiments)
associated with the pellet. The IN protein behaved differently in that
the protein from the wild-type virus was entirely associated with the
particulate fraction after detergent treatment and this distribution
was not altered by the L171I mutation. Although the exact structure of
the detergent-resistant material isolated from both infectious and
noninfectious virions remains to be determined, these results imply
that the intermolecular interactions that hold CA and RT in place in
the core have been altered in some way by the mutations. This finding
is consistent with the DNA synthesis defect identified in both infected
cells and cell-free virions.
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DISCUSSION |
With the addition of new mutations in this study, we present the
most comprehensive collection of such mutations, consisting of a total
of 25 substitutions placed at 10 positions (Fig. 1). A few
substitutions in this sequence, primarily alterations at the less
highly conserved positions in the motif, caused no demonstrable effects
on virus infectivity; these were not studied further. Two classes of
lethal mutations could be distinguished
those that caused a severe
assembly and release defect and others that allowed near-normal
particle release. Strikingly, the distributions of these two phenotypes
across this region of CA are almost identical. At five of seven
positions, replacement with two or more different amino acids yielded
both types of noninfectious mutants. Only at Q158 did all five
replacements destroy assembly (see section below). From this analysis,
there is no evidence for functionally distinct subregions within this
region of CA; rather, the entire domain probably functions as a whole.
This conclusion is quite significant, given the wide variety of
phenotypes that have been seen in HIV-1 and M-PMV MHR mutants
(31, 40).
Implications of the budding-defective phenotype.
The
block to release from avian cells in certain MHR mutants seems
contradictory to the published findings that the CA region of Gag is
not part of the minimal protein segments needed to drive budding, a
conclusion drawn from Gag expression studies in mammalian cells
(12, 29). However, the pattern of intracellular Gag proteins observed in avian cells with these mutants, i.e., minimal Gag
cleavage and very little CA protein in cell lysates (Fig. 2A)
(12), resembles that seen with Gag mutants that are
deficient in Gag-membrane binding (a function of Gag MA) or Gag-Gag
interaction (the NC region) (2, 13, 42). The budding
defect in the MHR mutants could conceivably result from interference
with either activity via long-range structural effects. However, our
experience with the modularity of these functions and the plasticity of
the RSV Gag to mutation (2, 13, 29, 43, 45) make this seem unlikely. An alternate scenario is that a localized structural perturbation within the CA carboxy-terminal domain (CTD) of Gag leads
to inappropriate aggregation of the precursors in the avian cell. Such
a dead-end pathway could also result from inappropriate interactions of
Gag with a cellular factor(s). This could explain the cell type
dependence of certain RSV MHR mutants, i.e., Gag proteins that allow
budding from mammalian cells but not avian cells (12).
Of the mutations that interfered with assembly, R170L and E162G and all
five replacements at the Q158 position alter the conserved hydrophilic
residues in the MHR. The homologous residues in the HIV CA protein form
an unusual network of hydrogen and ionic bonds that links the two
halves of the MHR to one another and to the
-helix immediately
following the MHR. Recently obtained nuclear magnetic resonance
spectroscopy data on the RSV CA CTD are consistent with the
presence of a similar network (28). The central role of
the glutamine in this network (20) suggests that it is
especially important for the folding of the CTD, and this may explain
why all substitutions at Q158 destroyed RSV assembly. The R170L and E162G substitutions that also interfere with assembly (12)
should likewise have dramatic effects on this bonding network. The more conservative substitutions (R170Q and E162D), on the other hand, may be
compatible with particle assembly and release because they are able to
maintain at least some of the hydrogen bond network. Thus, these
findings suggest that a similar bonding network forms in the Gag
precursor and is important for maintaining its assembly function. The
remaining budding-defective mutations are alterations that create
rather substantial changes in the hydrophobic core of the CTD. For
example, introduction of a polar amino acid (F167S) or of a larger,
bulkier hydrophobic residue (L171F) had dramatic effects on the
assembly of the Gag protein, supporting the idea that these changes are
destabilizing the hydrophobic core of the CTD.
Budding-competent, noninfectious mutants.
When the lethal
mutations that destroyed the budding capacity of Gag are removed from
consideration, all those that remain have a common feature
a defect in
reverse transcription. Many of these are the more conservative
substitutions placed at the same sites where more radical changes
blocked virus assembly. The L171I mutant is the most thoroughly
characterized. The disability in the other MHR mutants of this class,
although less severe in some cases, is qualitatively the same, as is
that of the D155Y mutant, whose substitution lies at the boundary of
the MHR and the interdomain linker.
The L171I particles contain properly processed Gag proteins and have
physical properties (size and density) identical to those of the
wild-type parent (12, 29). The Gag-Pol precursor is packaged and processed to form enzymatically active RT. The packaging and integrity of the viral genome also appear normal. What is not known
is whether the placement of tRNA on the primer binding site of the
viral RNA is qualitatively and quantitatively normal, but we have been
able to detect the presence of the primer on the viral RNA by end
labeling with [32P]dATP (data not shown). The ability of
the mutant virus to bind and enter cells has not been tested, although
failure of virus entry seems an unlikely explanation since Env
glycoproteins have been detected on the particles (12)
(data not shown) and there is no reason a priori to guess that CA
mutations would interfere with this step.
Defects consistent with the in vivo results were found in extracellular
mutant particles
a serious deficit in either the initiation of DNA
synthesis or the elongation of the nascent viral DNA and the disruption
of core integrity indicated by the ease of detergent extraction of CA
and RT. The first strand-switching step does not appear to be affected
by the mutations (with the possible exception of the L171A mutant);
however, it is not known whether extension of the DNA molecules after
this step occurs with normal efficiency. Finally, the defect in DNA
synthesis in infected cells exceeds that observed in the endogenous
reverse transcription reaction by a factor of 10, suggesting that the
instability of the mutant cores becomes even more critical in the
environment of the cytosol. It is possible that other, unidentified
factors are limiting the efficiency of strong-stop DNA formation in the cell. Regardless, the reduced endogenous reverse transcription activity
suggests that the phenotype of these RSV mutants may truly be different
from that of Fv-1-restricted MuLV (26, 38), HIV
CA mutants that fail to incorporate cyclophilin A (7), and
other MuLV CA mutants (1) that fail to make viral DNA in the cell although they are able to do so in extracellular particles.
Clearly, the primary function of the MHR is not one of packaging the
viral genome or the Gag-Pol precursor nor of controlling the
PR-mediated processing of Gag or Gag-Pol. The viral DNA synthesis deficit and the unusual detergent sensitivity of the cores in extracellular mutant particles (in spite of apparently normal incorporation and processing of the component parts) argue instead that
the defect is due to inappropriate interactions between the core
components. In other words, the parts are not put together properly. It
is tempting to conclude that this results from a failure of the MHR
residues to perform a normal activity that is needed for putting the
parts together. It must also be recognized, however, that the phenotype
could be an indirect consequence of structural abnormalities in Gag or
CA which interfere with the formation or activity of the viral core by
some means unrelated to the normal function of the MHR. Thus, although
characterization of these RSV mutants has eliminated a number of
possibilities from consideration, the question of the function of the
MHR residues in the wild-type virus remains open.
Structural studies of the CA proteins may yet yield some useful clues
to CA function. Work by Gamble et al. has described a CA-CA interface
in the CTD of HIV CA that appears to explain the dimerization activity
of both the isolated domain and the intact CA protein in solution
(20). This interface is expected to exist in the assembled
CA shell as well. In the HIV protein, the MHR does not appear to
participate directly in the CA-CA interface. However, this region is
integral to the CA CTD structure and is in intimate contact with the
-helix that forms the dimer interface (20, 46). In
vitro assembly studies with the HIV CA protein indicate that different
conformations correlate with different modes of protein packing
(22). Thus, it is quite conceivable that certain MHR
substitutions in the HIV protein could perturb the domain structure and
thereby alter CA-CA interactions. In the RSV mutants, a similar
scenario might explain the loss of detergent resistance in the virion
core as well as the lethal phenotype. However, the RSV protein, unlike
the one from HIV, fails to dimerize in solution (9, 28);
therefore, the possible consequences of the lethal MHR substitutions on
CA multimerization cannot be evaluated as yet.
The possibility that the MHR is critical to the structure of the Gag
precursor and the mature CA protein does not appear sufficient to
explain its unusually strong conservation. It may be significant that
the MHR immediately follows the flexible interdomain linker. It seems
quite possible that the MHR could be a conformational switch that
controls the interactions between CA subunits or heterotypic interactions that need to occur in an ordered fashion during
maturation. Such a dynamic role in the progression of events that
connects Gag assembly to the final formation of an active core might be consistent with the duality of mutant phenotypes observed. Finally, the
DNA synthesis defect in the mutants raises the interesting possibilities that the MHR is a site of interaction with other viral or
cellular factors necessary for vDNA synthesis and that CA could be a
direct contributor to the DNA synthesis machinery. Although we cannot
distinguish between these possibilities at this time, the field has
been narrowed considerably as a result of these studies, and the
contribution of CA to the DNA synthesis pathway will continue to be explored.
 |
ACKNOWLEDGMENTS |
Many thanks are due to John Wills for support, encouragement, and
constructive criticisms during this work. We also thank Volker Vogt,
Rich Kingston, and Michael Rossmann for sharing their structural models
of the RSV CA protein prior to publication. We appreciate the critical
review of the manuscript by Leslie Parent and Brad Bowzard. Brad
Bowzard also assisted this project by constructing the L171A proviral vector.
This work was supported by funds from the Four Diamonds Research Fund
(to R.C.C.) and by NIH grant R01 CA47482 (to J. W. Wills).
 |
FOOTNOTES |
*
Corresponding author. Mailing address: Department of
Microbiology and Immunology, The Pennsylvania State University College of Medicine, 500 University Dr., P.O. Box 850, Hershey, PA 17033. Phone: (717) 531-3528. Fax: (717) 531-6522. E-mail:
rcraven{at}psu.edu.
 |
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Journal of Virology, January 2001, p. 242-250, Vol. 75, No. 1
0022-538X/01/$04.00+0 DOI: 10.1128/JVI.75.1.242-250.2001
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