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Journal of Virology, March 2006, p. 2076-2082, Vol. 80, No. 5
0022-538X/06/$08.00+0 doi:10.1128/JVI.80.5.2076-2082.2006
Copyright © 2006, American Society for Microbiology. All Rights Reserved.
Departments of Neurology,1 Microbiology,University of Colorado Health Sciences Center, Denver, Colorado 80262,2 Graduate School of Medicine, Department of Microbiology, Research Foundation for Microbial Diseases of Osaka University, Kanonji Institute, 2-9-41 Yahata, Kanonji, Kagawa, Japan,3 National Institute of Biomedical Innovation, 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan,4 Laboratory of Clinical Infectious Diseases, National Institutes of Health, Bethesda, Maryland5
Received 16 September 2005/ Accepted 21 November 2005
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The VZV genome contains regions of inverted repeated DNA sequences; consequently, 3 open reading frame (ORF) pairs (ORF 62 and ORF 71, ORF 63 and ORF 70, and ORF 64 and ORF 69) are diploid. Thus, 37 of the 63 mutated sites between P-Oka and V-Oka genomic DNA are unique mutations located within 21 ORFs. Ten mutations are found within ORF 62, which encodes IE 62, the major immediate-early transactivator of VZV gene transcription. Previous transient-transfection-based studies suggested that IE 62 derived from V-Oka is a less potent transactivator of VZV genes than the P-Oka-derived IE 62 (7-9). Here, we used well-characterized PCR-based macroarrays (5) to compare the global virus gene transcriptional activity of both the parental and vaccine strains of VZV during lytic infection. Array data were confirmed at the RNA level by quantitative cDNA dot blot analysis and at the protein level by Western blot analysis. The ability of IE 62 derived from P-Oka and V-Oka to transactivate selected VZV gene promoters was also determined.
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RNA extraction. Cell pellets were thawed in Tri-Reagent (Molecular Research Center, Cincinnati, OH) and sonicated on ice three times for 10 s each, and 1-bromo,3-chloropropane was added to initiate phase separation. RNA was precipitated with a 0.5 volume of isopropanol for 20 min at room temperature, collected by centrifugation at 12,500 x g for 30 min at 4°C, washed in 70% ethanol, and dissolved in water. Residual DNA was digested with RNase-free DNase (DNA-free; Ambion, Austin, TX) at 37°C for 20 min. poly(A)+ RNA was extracted by oligo(dT) cellulose chromatography (NucleoTrap; Clontech, Palo Alto, Calif.). Lack of PCR amplification using VZV DNA-specific primers (5) confirmed the absence of DNA from the poly(A)+ RNA. poly(A)+ RNA (1 µg) was primed with oligo(dT) for cDNA synthesis (SuperScript II; Invitrogen, Carlsbad, Calif.). After incubation at 37°C for 90 min, enzyme was inactivated at 65°C for 5 min and cDNA was cleaned by microfiltration (Microcon-PCR; Millipore, Bedford, Mass.).
VZV macroarrays. Construction and validation of PCR-based VZV macroarrays has been described previously (5). Briefly, 300- to 600-bp segments of the VZV genome mapping to the 5' and 3' ends of all predicted VZV ORFs were PCR amplified, inserted into pGEM3zf , and used to generate (by PCR amplification with universal vector-specific primers) target DNA. Target DNA was manually spotted on nylon-based membranes, alkaline denatured, UV cross-linked, and stored under a vacuum until use.
cDNA probe synthesis and hybridization. For each sample, 100 ng cDNA was labeled with [32P]dCTP by nick translation (Rediprime II; Amersham Pharmacies Biotech, Piscataway, N.J.). Individual labeling reaction mixtures containing 25 ng cDNA and 10 µCi [32P]dCTP were incubated at 37°C for 60 min. Unincorporated isotope was removed by gel filtration (Micro Bio-Spin P30; Bio-Rad, Hercules, Calif.). Probes were heat denatured, quenched on ice, and added to prehybridized arrays in 20 ml Perfecthyb (Sigma-Aldrich, St. Louis, Mo.). Hybridization was for 48 h at 62°C, after which the arrays were washed at 62°C three times at low stringency (2x SSC [1x SSC is 0.15 M NaCl plus 0.015 M sodium citrate], 0.1% sodium dodecyl sulfate [SDS]), twice at high stringency (0.5x SSC, 0.1% SDS), and once at ultra-high stringency (0.1x SSC, 0.1% SDS). Arrays were air dried and exposed for uniform times to phosphorimager screens (Molecular Dynamics, Piscataway, N.J.).
Array data analysis.
The signal intensity, reflecting the
amount of 32P-labeled cDNA that bound to each array target,
was quantitated by densitometric scanning (ImageQuant; Molecular
Dynamics). The formula used to determine the transcriptional activity
for each ORF (5) was
modified as follows to reflect the expression level for each P-Oka ORF
relative to the same V-Oka ORF: RE =
(
i/
c)/(
i/
c)
where RE is the relative expression,
i is
the average intensity of VZV ORF target (i) probed with
32P-labeled P-Oka cDNA,
c is the
average intensity of control targets (actin, glyceraldehyde 3-phosphate
dehydrogenase [GAPdH], no DNA, and plasmid DNA) probed with
32P-labeled P-Oka cDNA,
i is the
average intensity of VZV target (i) probed with the
32P-labeled V-Oka cDNA, and
c is
the average intensity of control targets (actin, GAPDH, no DNA, and
plasmid DNA) probed with the 32P-labeled V-Oka
cDNA.
Dot blot analysis. First-strand cDNA was synthesized from mRNA extracted from either P-Oka- or V-Oka-infected MRC-5 cells, spotted onto nylon-based charged membranes (Zeta probe; Bio-Rad), air dried, and UV cross-linked. Recombinant plasmids containing cloned inserts specific to cellular beta-actin and VZV ORFs 41, 62, and 66 were propagated, and the inserts were excised, gel purified, and radiolabeled with 32P by nick translation. Quadruplicate cDNA spots containing cDNA from each sample were probed with the respective plasmid-derived insert, washed, and exposed to phosphorimager screens, and the amount of 32P-labeled probe hybridizing to each individual target was determined by densitometric scanning (ImageQuant; Molecular Dynamics).
Western blots.
MRC-5 cells in T75 flasks were
infected with equal titers of P-Oka or V-Oka, passaged onto uninfected
MRC-5 cells in T175 flasks (1 infected cell: 6 uninfected cells), and
harvested 3 days later. After treatment with trypsin and washing with
complete medium followed by a phosphate-buffered saline wash, cells
were lysed in RIPA buffer (10 mM Tris-Cl, pH 8, 100 mM NaCl, 1 mM EDTA,
1% NP-40, 0.5% deoxycholic acid, 0.5% SDS) with TLCK
[L-1-chloro-3-(4-tosylamido)-7-amino-2-heptanone
hydrochloride, N-
-tosyl-L-lysine
chloromethyl ketone], TPCK
[L-1-chloro-3-(4-tosylamido)-4-phenyl-2-butanone
tosyl-L-phenylalanine chloromethyl ketone], and Roche
Complete protease inhibitor cocktail (Roche Diagnostics Corp.,
Indianapolis, Ind.) and boiled in SDS loading buffer. Proteins were
resolved by electrophoresis on SDS-polyacrylamide gels and transferred
to Nytran membranes (Schleicher & Schuell Biotechnology, Keene,
N.H.), and the blots were probed with rabbit antiserum directed against
VZV ORF 65 (4) or ORF 66
(11) proteins, IE 62
(16) or gE (Chemicon
International, Temecula, Calif.). Blots were developed using enhanced
chemiluminescence (Pierce Biotechnology, Inc., Rockford, Ill.), and
bands corresponding to VZV proteins were quantified using a
phosphorimager (Molecular Dynamics). Multiple levels of standardization
were used in the Western blot analysis. First, equal numbers of cells
were analyzed. Second, to take into account any slight differences in
virus spread in culture, the amount of gE present in the protein
samples was determined. Controlling for the level of infection is more
important than controlling for the amount of protein per se, since not
all cells in the culture are infected. Finally, all Western blot
analyses were done in replicate, and the results are presented as
average (± standard deviation) relative protein
expressions.
Promoter activity assay. The transactivational activity of P-Oka- and V-Oka-derived IE 62 on six VZV gene promoters was determined in transient-transfection assays (7, 8). VZV gene promoters were directionally inserted into the luciferase reporter plasmid, pGL3basic (Promega). All promoter regions reflect the intergenic segment separating the opposing ORFs. Thus, the promoters for ORFs 20 and 21 are contained within the same 284-bp DNA segment mapping from 30,476 to 30,758 bp on the VZV genome (Dumas strain, accession number NC_001348), ORF 28 and 29 promoters map to the 221 bp between 50,637 and 50,856, and ORF 65 and 66 promoters are contained within 397 bp between 112,641 and 113,036. DNA sequence analysis of P-Oka (accession number AB097932), V-Oka (accession number AB097933), and the Dumas strain of VZV indicates complete sequence homology between these three genomes in the promoter regions for VZV genes 20, 21, 28, 29, 65, and 66. The effector plasmids consisted of ORF 62 with cognate promoter from either P-Oka or V-Oka inserted into pUC-19. Thus, the effector plasmids expressed IE 62 derived from P-Oka (P-IE 62) or from V-Oka (V-IE 62). The 10 mutations found in V-Oka ORF 62 are also present in V-Oka ORF 71 (9), and three of the 10 V-Oka ORF 62/71 mutations display sequence polymorphism, emphasizing the polyclonal nature of V-Oka. The V-Oka ORF62 expression plasmid used in transient-transfection assays was selected to contain all 10 nucleotide and 8 amino acid changes within the IE 62 protein coding segment (7). For transient transfections, various amounts (0 to 2 µg) of effector plasmid were transfected into CV1 cells together with one of the reporter plasmids. The transfection efficiency was normalized to total protein concentration of each cell lysate. The relative induction for each VZV promoter construct was calculated compared to controls consisting of reporter plasmid alone. All promoter assays were done in duplicate on independent samples with similar results. P-Oka- or V-Oka-derived IE 62 differentially activates transcription (see Fig. 2 below), resulting in different levels of IE 62 protein (see Fig. 3 below), which could result in autoactivation of IE 62 during transfection. However, to be consistent with previously published results concerning P-Oka- and V-Oka-derived IE 62 activation of gene transcription (7, 8), transfection experiments were performed with increasing amounts of effector plasmid showing a dose response activation of all VZV gene promoters. For transient transfections, various amounts (0 to 2 µg) of effector plasmid were transfected into CV1 cells together with one of the reporter plasmids. In initial experiments, MRC-5 cells were used as targets for transfections; however, the efficiency of DNA uptake in these cells was very low. Thus, to be consistent with previous data (7), CV1 cells were used for transfections. In addition, 293 cells were used previously for transient transfection and VZV gene promoter induction with P-Oka- and V-Oka-derived IE 62 with similar results (9).
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FIG. 2. Relative
expression of each predicted VZV ORF. Panel A shows the steady-state
level of each VZV ORF determined by densitometric scanning of the
transcriptional macroarray. The ratio (relative expression) of P-Oka
ORF expression compared to the corresponding V-Oka ORF expression level
indicates that the steady-state levels of VZV ORFs 62, 65, 66, and 67
are significantly higher and that of ORF 41 is significantly lower
(P < 0.01) than the overall average relative
expression of all VZV ORFs. Panel B shows the dot blot analysis of VZV
ORFs 41, 62, and 66. The extent of hybridization was determined and
normalized to cellular actin. The relative expression for each ORF in
P-Oka- or V-Oka-infected cells was compared. Consistent with the array
analysis, ORF 41 was underexpressed and ORFs 62 and 66 were
overexpressed in V-Oka-infected MRC-5
cells.
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FIG. 3. Western
blot analysis of P-Oka- and V-Oka-infected MRC-5 cells. Protein lysates
prepared from P-Oka- and V-Oka-infected MRC-5 cells were analyzed by
Western blotting for expression of VZV ORF 62 (62P), 65 (65P), and 66
(66P) protein. Compared with expression of VZV ORF 68 (gE), levels of
62P (1.96), 65P (1.65), and 66P (1.23) were greater in P-Oka-infected
cells than in V-Oka-infected
cells.
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FIG. 1. Transcriptional
array analysis of P- and V-Oka VZV-infected MRC-5 cells. Two
independent sets of mRNA were extracted from P-Oka and V-Oka
VZV-infected MRC-5 cells and processed for analysis on PCR-based
macroarrays as described in Materials and Methods. Results for 16
arrays (8 for each virus) are shown. Densitometric scanning revealed a
significant difference in the steady-state level of ORF 62, 65, 66, and
67 transcription compared to cellular controls. The location of VZV ORF
62, 65, 66, and 67 target spots and cellular actin and GAPdH target
spots is shown on representative arrays. Boxed ORF spots indicate
transcripts suppressed in V-Oka-infected
cells.
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View this table: [in a new window] |
TABLE 1. Relative
expression of VZV ORFs
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Transactivation of specific VZV promoters by P- and V-Oka-derived IE 62. Transient-transfection assays were performed to compare the response of the VZV ORF 65 and 66 promoters to P-IE 62 and V-IE 62. Reporter plasmids were constructed to place luciferase synthesis under the control of VZV ORF 20, 21, 28, 29, 65, and 66 promoters. ORF 20, 21, 28, and 29 promoters were used as controls, since they are of lengths similar to those of the ORF 65 and ORF 66 promoters and because the steady-state levels of ORF 20, 21, 28, and 29 transcripts in both P-Oka- and V-Oka-infected cells are similar (Table 1). All promoters showed an increase in activity with increasing amounts of IE 62 and a slight, but not statistically significant, increase in activity when transactivated by P-IE 62 compared to V-IE 62 (Fig. 4).
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FIG. 4. Transactivation
of VZV promoters by IE 62 derived from P-Oka or V-Oka VZV. The promoter
regions for VZV ORFs 20, 21, 28, 29, 65, and 66 were inserted into the
luciferase reporter plasmid, pGL3Basic. Since the promoter regions are
contained within intergenic DNA segments separating the opposing ORFs,
the promoters for ORFs 20 (pro20) and 21 (pro21) are contained within
the same 284-bp DNA segment, the promoters for ORFs 28 (pro28) and 29
(pro29) are both contained within the same 221-bp segment, and the
promoters for ORFs 65 (pro65) and 66 (pro66) are within the same 397-bp
segment. Transcription originating from all promoter regions was
transactivated with increasing amounts (from 0 to 2 µg) of
plasmid expressing IE 62 derived from P-Oka (pIE 62) or V-Oka (vIE 62)
VZV. The transactivating ability of pIE 62 (solid lines) was slightly
greater than that of vIE 62 (dotted lines) for the same promoter but
was not statistically
significant.
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Transient-transfection assays have shown that wild-type P-IE 62 is a better transactivator of selected VZV genes than V-IE 62 (7, 8). We have extended these findings to show that the steady-state level of all VZV genes is increased on average 1.19-fold in P-Oka-infected cells compared to V-Oka-infected cells in tissue culture. Further, the steady-state level of VZV ORF 62 transcription is significantly decreased in V-Oka-infected cells, along with a decrease in IE 62 protein. Thus, with respect to IE 62 transactivation of virus genes, mutations within V-Oka IE 62 result in a slight overall decrease in transcription of all VZV genes, a significant decrease in V-Oka ORF 62 transcription, and a concomitant reduction in IE 62 protein. ORF 66 transcripts and ORF 66 protein levels were also decreased in V-Oka-infected cells, making it likely that less IE 62 is incorporated into infectious V-Oka virions. Together, the reduced amount of IE 62 and ORF 66 protein might contribute to V-Oka attenuation.
Transient-transfection assays were performed to determine whether the reduced amounts of ORF 66 transcripts in V-Oka-infected cells compared to P-Oka-infected cells might reflect a reduced ability of V-IE 62 to activate the ORF 66 promoter. Control reporter constructs included the promoters for ORFs 20, 21, 28, 29, and 65. All promoter regions consisted of the intergenic segment separating the ORF pairs (ORFs 20/21, ORFs 28/29, and ORF 65/66), and DNA sequences in the P-Oka and V-Oka genomes do not differ within these promoter regions. In contrast with a previous report of the reduced ability of V-IE 62 to activate transcription from VZV ORF 28 and 29 promoters (7), we found no statistically significant difference in the ability of P-IE 62 or V-IE 62 to activate transcription from any of the promoter regions tested. In that study, CV-1 cells were transfected with promoter constructs consisting of approximately 750 bp of upstream VZV DNA sequences, and promoter activity was monitored based on chloramphenicol acetyltransferase activity. Since the same effector plasmids (P-IE 62 and V-IE 62) were used in both studies and all assays were performed in the same respective laboratory, the apparent discrepancy in activation of ORF 28 and 29 by V-IE 62 most likely reflects the presence of upstream regulatory sites in the DNA sequences external to the intergenic region.
Transcriptional array and Western blot analyses also revealed reduced expression of VZV ORF 65 in V-Oka-infected cells compared to P-Oka-infected cells. VZV ORF 65 encodes a nonessential virion protein that localizes to the Golgi apparatus (4, 25).
The
steady-state level of VZV ORF 67 transcripts was significantly reduced
in V-Oka-infected cells compared to P-Oka-infected cells. VZV ORF 67
encodes glycoprotein I (gI), one of seven glycoproteins present in
VZV-infected cells. VZV gI is homologous to herpes simplex virus type 1
gI (10). In both viruses,
this small (
40 kDa) protein forms a complex with the
neighboring gene product (gE for VZV and gE for herpes simplex virus
type 1). This complex binds the Fc fragment of immunoglobulin and is
involved in correct sorting of the virus to tight junctions for
cell-to-cell spread (12,
13,
28). Reduced VZV gI
reduces the spread of V-Oka in tissue culture cells
(2,
20). The external domains
of gI and gE associate, resulting in heterodimer formation
(14). The gI:gE complex
present in the trans-Golgi network (TGN) cycles to the cell
membrane and returns to the TGN via endocytosis
(1,
26). VZV gE is the most
abundant VZV glycoprotein and is essential for virus propagation
(10,
21). In the absence of
gI, normal gE trafficking is disrupted, resulting in the formation of
abnormal polykaryocytes with adherent TGN and reduced syncytium
formation, significantly reducing yields of infectious virus
(19,
26). While gI null VZV
can grow in melanoma and human embryonic lung fibroblast cells, albeit
with reduced yields of infectious virus
(2,
19,
21,
33), gI is required for
virus growth in human skin and thymus/liver (T-cell) implants
(22). Thus,
down-regulation of gI in V-Oka-infected cells may limit gI:gE complex
formation and result in reduced delivery of gE to the membrane, which
could be especially important as a mechanism by which V-Oka is
attenuated
The common function of the VZV genes whose expression is diminished in V-Oka-infected cells (ORFs 62, 65, 66, and 67) is related to assembly and spread of infectious virus. Thus, attenuation of V-Oka is not solely the result of mutational events clustered within IE 62 but may include reduced expression in VZV ORFs 65, 66, and 67 that together reduce assembly and spread of virus. Such a notion is supported by recent studies in which overlapping cosmid sets were used to generate recombinant VZV; chimeric VZV containing P-Oka-derived sequences covering ORFs 30 to 55 on a V-Oka background displayed wild-type infectivity in skin xenografts (34). Together, the data suggest that diminished vaccine virus virulence reflects a combination of mutations acting to reduce V-Oka replication.
We thank Paul Kinchington for IE62 antibody, Marina Hoffman for editorial assistance, and Cathy Allen for manuscript preparation.
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