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Journal of Virology, August 2008, p. 7411-7421, Vol. 82, No. 15
0022-538X/08/$08.00+0 doi:10.1128/JVI.00651-08
Copyright © 2008, American Society for Microbiology. All Rights Reserved.

Emory Vaccine Center and Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia 30322
Received 24 March 2008/ Accepted 8 May 2008
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Infection of mice with MHV68 leads to acute virus replication in a number of anatomical sites, including the lungs and spleen, with peak viral titers observed between days 5 and 10 postinfection and viral clearance by the host adaptive immune response between days 9 and 15 postinfection (4, 31). Upon resolution of the lytic infection, a latent infection in B lymphocytes, macrophages, and dendritic cells is apparent. Like with EBV infection, long-term latency is primarily restricted to germinal center and memory B lymphocytes (7-9, 28-30, 40).
The M2 open reading frame (ORF) is located at the left end of the MHV68 genome. It shares positional homology to latency-associated genes in other gammaherpesviruses (26, 34, 36). Studies of M2 translational stop mutants revealed that the M2 ORF is not required for acute virus replication in the lungs but plays a critical role in the establishment of splenic latency following low-dose intranasal inoculation (11, 13, 24). Increasing the inoculating dose partially restores establishment of splenic latency, but under these conditions there is a severe defect in virus reactivation from latently infected B cells (11, 13, 24). Thus, determining how the M2 gene is regulated during different stages of infection and in various cell types is important for determining the role of M2 in viral latency and for identifying possible therapeutic targets for interrupting latency in infected hosts.
The M2 gene product is a unique protein with no known homologs in viruses, mice, or humans. It contains an actively recognized CD8+ T-cell epitope that constitutes an important target for controlling the establishment of latent infection (12, 32, 33). Sequence analysis of M2 identified 9 PxxP motifs, characteristic of SH3 binding motifs, and a central positively charged region, leading to the hypothesis that M2 may manipulate signal transduction pathways. Indeed, specific key SH3 binding motifs and tyrosine phosphorylation motifs contribute significantly to the establishment of latency and reactivation in vivo (10). In vitro studies have demonstrated that the M2 protein has a cell-type-dependent localization and effectively inhibits interferon-mediated signal transduction by downregulation of STAT1/2 expression (15). Additionally, M2 interacts with the DDB1/COP9/cullin repair complex and ATM in fibroblast cultures, suppressing DNA damage-induced apoptosis (14). In B-cell lines M2 activates the Vav1/Rac1 pathway through a trimolecular complex with Vav1 and Fyn, leading to enhanced Vav1 phosphorylation (19, 22). M2 expression in primary B cells leads to interleukin-10 (IL-10)-dependent B-cell proliferation and secretion of IL-10, IL-2, MIP-1a, and IL-6 (23). Primary B cells expressing M2 differentiate into a preplasma memory B-cell phenotype, an intermediate differentiation state between plasma and memory B cells (23). Additionally, infection with an M2 null MHV68 (M2.Stop) leads to a significant decrease in serum IL-10 levels at day 16 postinfection, correlating with an increase in the frequency of MHV68-specific CD8 T cells (23).
Initial analysis of the M2 transcript revealed a spliced transcript composed of two exons, i.e., a noncoding 110-nucleotide (nt) 5' exon and a 1,235-nt 3' exon that contains the M2 ORF, and a 656-nt 3' untranslated region (12). Here we report the analysis of M2 gene transcription in latently infected mice, along with the subsequent mapping of M2 gene promoter activity in vitro and analysis of M2 promoter mutants in vivo. In addition, we identified a novel transcript arising from the region of the M2 gene, which contains a short ORF (M2b). However, analysis of viruses lacking an intact M2b failed to identify a role for this putative gene product in MHV68 infection. Finally, we constructed M2 splice acceptor and splice donor mutants that demonstrate the importance of the observed M2 splice acceptor site and the flexibility of M2 splice donor sites.
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Generation of virus mutants.
Mutations were introduced with overlap PCR mutagenesis using the wt MHV68 BAC (1) as a template. For the M2 promoter deletion viruses, a common set of outer primers, 5366_D_NsiI (5' GATCATGCATGTCTTCTTCCCCACGCGCACCAG 3') and 6569_C_NsiI (5' GATCATGCATGCCAGATCCCCGGTCTGTAAGAAC 3'), was used in combination with unique inner primer pairs as follows: for
5925-6014, 5924-5898_C (5' GAAGAGACTTTCAGCTTTCGGGAAGGG 3') and 5910-5924_6015-6041_D (5' GCTGAAAGTCTCTTCCTTTATTTTTAACAAAAAAATTTCCTC 3'); for
5925-5969, 5924-5898_C (5' GAAGAGACTTTCAGCTTTCGGGAAGGG 3') and 5910-5924_5970-5993_D (5' GCTGAAAGTCTCTTCGGAGATGGGTCAAAACCACCTGAC 3'); for
5861-5925, 5860-5835_C (5' GTCTCTTCTGGGTGAAGCGGTGTTAC 3') and 5847-5860_5926-5953_D (5' CACCCAGAAGAGACGCTAGTCAAGCGTGGTGCAGACCTCATG 3'); and for
5861-6014, 5860-5835_C (5' GTCTCTTCTGGGTGAAGCGGTGTTAC 3') and 5847-5860_6015-6046_D (5' CACCCAGAAGAGACCTTTATTTTTAACAAAAAAATTTCCTCTTAAG 3'). For the M2 splice acceptor mutant, outer primers 3964-3987_D (5' GTCACGCTTCTCCTTCCAGGCGTG 3') and 5208-5184_C (5' GGTGAAATCCTGGGGACTTCTAGAG 3') were used with inner primers 4592-4625_D (5' GGGTGTTGGGGCCATGCTTTGAAAACGAAACCTC 3') and 4625-4592_C (5' GAGGTTTCGTTTTCAAAGCATGGCCCCAACACCC 3') to introduce the underlined 4-bp mutation, which disrupts the M2 splice acceptor and introduces an NlaIII restriction site. For the M2 splice donor mutant, outer primers 5199-5222_D (5' GGATTTCACCTAGTCCTTGCCGGC 3') and 6415-6391_C (5' GCTACTACAAGTACAGCGTGAGCCC 3') were used with inner primers 5799-5833_D (5' GGCCCAGAATACATCGAGCCCTGTGCGTGAGAGTC 3') and 5833-5799_C (5' GACTCTCACGCACAGGGCTCGATGTATTCTGGGCC 3') to introduce the underlined 4-bp mutation, which disrupts the M2 splice donor site and introduces a BanII restriction site. For the M2b.Stop mutation, M2bSTOP_5182_D (5' GATCAGATCTCTCTCTAGAAGTCCCCAGGATTTC 3') and M2bSTOP_6382_C (5' GATCGCGGCCGCCCATGGACCACTTGATCCTAG 3') were used with inner primers M2bSTOP_5782_D (5' CCCACCATTCCCTCTTAGGTCTAGACTACATACCACCCTG 3') and M2bSTOP_5821_C (5' CAGGGTGGTATGTAGTCTAGACCTAAGAGGGAATGGTGGG 3') to introduce the underlined mutations, which introduce a translational stop codon and an XbaI restriction site after the initiation codon. Each mutant PCR product was cloned into pCR Blunt vector (Invitrogen) and sequenced to verify mutations. Recombinant viruses were generated by allelic exchange in Escherichia coli as previously described (17, 25). Briefly, the NsiI restriction sites within the pCR Blunt vector were used to excise the MHV68 fragment. The fragment was cloned into the suicide vector pGS284, which contains an ampicillin resistance cassette and a levansucrase cassette for positive and negative selection, respectively. The resulting targeting vectors were transformed into S17
pir E. coli cells and mated to GS500 E. coli (RecA+) harboring wt MHV68 BAC. Cointegrants were selected on Luria-Bertani (LB) agar plates containing chloramphenicol at 17 µg per ml and carbenicillin at 50 µg per ml and were resolved following overnight growth in liquid LB medium containing only chloramphenicol. Bacterial cells were then plated on LB agar plates containing chloramphenicol and 7% sucrose to select for loss of the levansucrase cassette (and thus the pGS284 vector sequence). Colonies were screened by PCR for a reduction in size for the promoter mutants or for the introduction of the diagnostic restriction site for the M2b.Stop mutation, the M2 splice acceptor mutation, and the M2 splice donor mutation. Positive clones were grown in LB medium with chloramphenicol, and BAC DNA was purified with a MidiPrep kit (Qiagen, Hilden, Germany) as described by the modified manufacturer's protocol. The presence of the desired mutations was further confirmed by amplifying sequence outside of the targeting region (100 bp on either side of the homology arms) by PCR, cloning into the pCR Blunt vector, and sequencing with vector-specific primers.
RACE analysis. RNA was harvested from pooled splenocytes of five mice harvested at day 16 post-intranasal infection with 100 PFU wt virus. Approximately 2 x 108 cells were lysed with guanidine isothiocyanate-phenol solution (GITC-phenol, 2 M guanidine isothiocyanate, 0.05 M β-mercaptoethanol, 0.25% sarcosyl, 0.1 M Na acetate) followed by extraction with chloroform. RNA was precipitated with isopropanol and resuspended in RNase-free water. Rapid amplification of cDNA ends (RACE) was performed using the GeneRacer system (Invitrogen). The sequence of the gene-specific oligonucleotide primer used for round 1 5' RACE, 4285-4309_D, was 5' CTTCAGGACTTGGTACAGGACTCGG 3'; that for round 2 5' RACE, 4391-4415_D, was 5' CAAAGGCGGGCGCTGAGGTCTGCCC 3'. The sequence of the gene-specific oligonucleotide primer used for round 1 3' RACE, 5918-5893_C, was 5' GACTTTCAGCTTTCGGGAAGGGTTTAG 3'; that for round 2 3' RACE, 5888-5864_C, was 5' TTCCCCTCTCAAGCTGCTTCCTTAG 3'. PCR products were electrophoresed on 1% agarose gels, and specific bands were excised and prepared for ligation using a Qiagen gel extraction kit (Qiagen, Valencia, CA). Products were subcloned into pCR4-TOPO (Invitrogen) and analyzed by DNA sequencing. RACE analysis was repeated three times from independent mouse infections.
Plasmids. M2 promoter reporter plasmids were constructed by PCR amplification of the indicated sequences from a wt MHV68 BAC DNA template with XhoI restriction sites incorporated in both the forward and reverse primers. PCR products were purified by gel extraction, digested with XhoI, and cloned into the XhoI site of the pGL4.10 luciferase reporter vector (Promega Corporation, Madison, WI). The orientation of the inserted sequence was verified by PCR with vector-specific primer pGL4.10_D (5' CTAGCAAAATAGGCTGTCCCC 3') or pGL4.10_C (5' GCGTAGGTAATGTCCACCTCG 3') with the insert-specific primer M2-103_6027C (5' GATCCTCGAGGTTAAAAATAAAGTTATTTTTAAAAAAGATACGAG 3'). Upstream primer M2-1000_6924C (5' GATCCTCGAGCTCTGTGGGTGGCACACCAGTG 3'), M2-500_6424C (5' GATCCTCGAGCTTGCCCATGCTACTACAAGTAC 3'), M2-203_6127C (5' GATCCTCGAGCTAACCTGGTTGGGGTCAGCTTGATG 3'), or M2-103_6027C (5' GATCCTCGAGGTTAAAAATAAAGTTATTTTTAAAAAAGATACGAG 3') was used with downstream primer M25'_5924D (5' GATCCTCGAGCTGCTAGTCAAGCGTGGTGCAGACC 3'), M2 + 50_5875D (5' GATCCTCGAGGCTTGAGAGGGGAAGTGCCTAAAC 3'), M2 + 75_5850D (5' GATCCTCGAGCCAGAAGAGACTGGCTAAGGAAG 3'), or M2 + 100_5825D (5' GATCCTCGAGGTGAGAGTCTGTAACACCGCTTC 3') to construct the array of reporter fragment lengths.
Luciferase reporter assays. WEHI231 or S11 cells were grown to confluence under the conditions described above. Reporter constructs were transfected with a Nucleofector I device (Amaxa, Inc., Gaithersburg, MD) according to manufacturer's protocol. Briefly, cells were counted to determine density, spun down, and resuspended at 1 x 106 cells per 100 µl of the appropriate Nucleofector solution (solution V for S11 cells and solution R for WEHI231 cells). Five micrograms of reporter plasmid DNA in 5 µl water was mixed by gentle pipetting with 100 µl of cell suspension; the sample was placed in an Amaxa cuvette and subjected to the appropriate transfection program in the Nucleofector I device (program O-17 for both S11 and WEHI231 cells). Cells were transferred from the cuvette to a 12-well tissue culture plate and cultured in 2 ml RPMI 1640. The green fluorescent protein expression plasmid pmaxGFP (Amaxa) was used to measure nucleofection efficiency by fluorescence microscopy. At 48 h postnucleofection, cells were scraped from the wells and spun down. Cell pellets were lysed in 200 ml passive lysis buffer (Promega) for 20 min at room temperature. Fifty microliters of lysate was used to assay luciferase activity with a luciferase reporter assay system (Promega) according to the manufacturer's protocol. Transfections and luciferase assays were performed independently in triplicate at least two times.
Mice, infections, and organ harvests. Female C57BL/6J mice (catalog no. 000664; The Jackson Laboratory, Bar Harbor, ME) were housed at the Yerkes or the Whitehead vivarium in accordance with university and federal guidelines. Mice between the ages of 8 and 12 weeks were placed under isofluorane anesthesia prior to intranasal inoculation with 100 PFU of virus in 20 µl of cMEM. Spleens were harvested into cMEM, homogenized, and filtered through a 100 µm-pore-size nylon strainer (Becton Dickson, Franklin Lakes, NJ). Erythrocytes were eliminated with red blood cell lysis buffer (Sigma, St. Louis, MO). Splenocytes were pooled from five mice in all experiments. Lungs were harvested in cMEM and stored at –80°C.
Plaque assay. Plaque assays were performed as previously described (5) with the following modifications. Six-well plates were seeded with 2 x 105 NIH 3T12 cells per well at 24 h prior to infection. Mechanical disruption of lungs was performed in four rounds of 1 minute each using 1.0-mm zirconia/silica beads (Biospec Products, Bartlesville, OK) in a Mini-Beadbeater-8 (Biospec Products). Serial 10-fold dilutions of lung homogenate were plated on NIH 3T12 monolayers in a 200-µl volume. Infections were performed at 37°C for 1 hour with rocking every 15 min. Following infection, monolayers were covered with 5 ml cMEM containing 2% methylcellulose. At 6 or 7 days following infection, plates were stained with a neutral red overlay, and plaques were counted the following day. The limit of detection for this assay is 50 PFU.
LD ex vivo reactivation analyses. Limiting-dilution (LD) analysis to determine the frequency of cells harboring virus capable of reactivating from latency was performed as previously described (37, 39). Briefly, splenocytes were resuspended in cMEM as described above and plated in serial twofold dilutions (starting with 1 x 105cells) onto MEF monolayers in 96-well tissue culture plates. Twelve dilutions were plated per sample, and 24 wells were plated per dilution. Wells were scored for cytopathic effect (CPE) at 21 days postplating. The presence of preformed infectious virus was determined by plating parallel samples of mechanically disrupted cells (latent virus cannot reactivate from killed cells) onto MEF monolayers (37-39). The level of sensitivity of this assay is 0.2 PFU (37).
LD-PCR detection of the frequency of cells harboring the viral genome. LD analysis to determine the frequency of cells harboring the viral genome was performed using a nested PCR assay with single-copy sensitivity as previously described (38, 39). Briefly, splenocyte samples were counted, washed, resuspended in isotonic buffer, and plated in serial threefold dilutions in a background of 1 x 104 uninfected NIH 3T12 cells in 96-well plates (MWG Biotech, High Point, NC). Plates were covered with PCR foil (Eppendorf Scientific, Westbury, NY). Cells were lysed with proteinase K for 6 h at 56°C. Ten microliters of round 1 PCR mix was added to each well by foil puncture. Upon completion of the first round of PCR, 10 µl of round 2 PCR mix was added to each well by foil puncture. Following the second round of PCR, products were resolved by ethidium bromide staining on 2% agarose gels. Cell lysis and PCR were performed on a PrimusHT thermal cycler (MWG Biotech, High Point, NC). Twelve PCRs were performed for each sample dilution, and six dilutions were performed for each sample. Each PCR plate contained control reactions (uninfected cells or 10 copies, 1 copy, or 0.1 copy of target plasmid DNA in a background of 1 x 104 cells) as previously described (38, 39). All LD-PCR assays demonstrated approximately single-copy sensitivity without false positives.
Statistical analyses. Data were analyzed with GraphPad Prism software (GraphPad Software, San Diego, CA). Data were subjected to nonlinear regression analysis to determine the single-cell frequency for each LD analysis. From the Poisson distribution, the frequencies of reactivation and viral genome-positive cells were obtained from the nonlinear regression fit of the data where the regression line intersected 63.2%.
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FIG. 1. (A) Identification of M2 gene transcription start sites. 5' and 3' RACE analyses were performed using nested primer sets on 5'-capped poly(A) RNA prepared from bulk splenocytes harvested at day 16 postinfection as described in Materials and Methods. The locations of the RACE primers are indicated by black arrows beneath the representation of the M2 transcript structure. 5' initiation sites are indicated by vertical arrows beneath the primary sequence, and the number of sequenced clones originating at the indicated sequence is listed below the arrow. (B) In silico analysis (http://www.cbil.upenn.edu/tess/) of potential transcription factor binding sites upstream of the proximal and distal transcription initiation sites.
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FIG. 2. Schematic overview of the region of the MHV68 genome carrying the M2 ORF. The locations of the M1, M2, M2b, and M3 ORFs are indicated by arrows. The three M2 transcripts, two spliced and one unspliced, are shown below the schematic of the viral genome. 3' RACE identified the termination site for the spliced M2 transcripts at bp 3378 and that for the unspliced M2b transcript at bp 5498. All the detected spliced M2 gene transcripts utilized the splice acceptor site at bp 4609 and the splice donor site at bp 5815.
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FIG. 3. Identification of an M2 promoter active in WEHI231 and S11 cells. Schematic illustrations of the M2 gene promoter constructs generated are shown beneath a map of the M3 gene and genomic sequences upstream of the M2 exon 1. The promoter constructs cloned were upstream of the firefly luciferase gene in the pGL4.10 reporter vector (Promega). The corresponding genomic coordinates, as well as the locations of M3 ORF and both M2 exon 1 species, are indicated above the reporter constructs. M2 promoter activity was assayed in WEHI231 and S11 cells. Each construct, or the control empty luciferase vector, was nucleofected into WEHI231 or S11 cells (see Materials and Methods). Fold induction in luciferase activity was calculated by dividing the luciferase activity observed with the indicated promoter constructs by that of empty vector. Error bars represent standard errors of the means from at least three independent experiments.
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5925-5969), two independently generated mutants were isolated to ensure that observed phenotypes were not due to spurious mutations at distal sites in the viral genome (Fig. 4).
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FIG. 4. Construction of M2 promoter mutant viruses. (A) The MHV68 BAC developed by Adler et al. (1) was used introduce the indicated deletions by RecA-mediated recombination (see Materials and Methods). (B) Southern blot analysis of M2 promoter mutant viruses. Deletion of the sequences from bp 5861 to 6014 and bp 5925 to 6014 removed both a KpnI and a DraI restriction site. Digests with these enzymes demonstrate the absence of these sites in the recombinant viruses. Deletion of the sequence from bp 5925 to 5969 resulted in the loss of the KpnI restriction site. A digest of this virus with KpnI does not cut, but the DraI site remains intact. Deletion of the sequence from bp 5861 to 5925 does not ablate either the DraI or KpnI site but does result in smaller fragments. This reduction in size is distinguishable in both digests. Sequencing 1.5 kb of sequence flanking both sides of the mutations confirmed specific deletion of the indicated sequence as well as the absence of second-site mutations. The probe contained sequence from genomic coordinates bp 4652 to 6559. Molecular size markers (1-kb DNA ladder; New England Biolabs, Beverly, MA) were run in the last lane.
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5861-5925), the distal promoter (
5925-5969 and
5925-6014), or both promoters (
5861-6014) (Fig. 4). To determine if the deletions in the M2 promoter region affected acute-phase virus replication, a multistep growth curve was performed (Fig. 5A and B). As expected, there was no statistical difference in the in vitro growth kinetics of any of the M2 promoter mutants compared to wt MHV68. Furthermore, no significant difference in acute virus replication in the lungs at day 9 postinfection was observed with any of the M2 promoter mutant viruses following intranasal inoculation with 100 PFU of virus (Fig. 5C). The latter results were expected since, as we have previously shown, there was no defect in acute replication of M2 null virus (M2.Stop) (13, 24).
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FIG. 5. M2 promoter mutants replicate with wt MHV68 kinetics in vitro and in vivo. (A and B) NIH 3T12 monolayers were infected with 0.05 PFU of the indicated virus. Wells were harvested at the indicated time points, and virus titers were determined on NIH 3T12 cells (see Materials and Methods). Error bars represent standard errors of the means from three independent experiments. (C) C57BL/6J mice were infected with 100 PFU of indicated virus. Lungs were harvested at day 9 postinfection, and viral titers were determined by plaque assay (see Materials and Methods). The data were compiled from two independent experiments, and each symbol represents the viral titer determined from an individual mouse infected with the indicated virus. The horizontal dashed line indicates the limit of detection of the assay (50 PFU/ml).
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5861-6014, established latency at a lower frequency than the mutants with smaller deletions. Notably, none of the deletions clearly distinguished the importance of the proximal and distal transcription initiation sites. This may reflect the presence of cis-regulatory elements that are required for both upstream and downstream transcription initiation sites. Importantly, even the largest M2 promoter deletion (
5861-6014), although significantly reduced in establishment of latency compared to wt virus, did not exhibit as severe a defect as the M2.Stop mutant (Table 1 and Fig. 6C). This raises the possibility that there may be an alternatively mechanism for generating M2 gene expression, which could reflect either transcription from a cryptic promoter(s) that is revealed when the identified M2 promoter(s) is deleted or an alternative bona fide M2 gene promoter. Importantly, to date none of our 5' RACE analyses of wt MHV68-infected splenocytes have identified the presence of any alternatively initiated M2 gene transcripts. |
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TABLE 1. Frequencies of viral genome-positive and reactivating splenocytes at day 16 postinfection
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FIG. 6. Analysis of virus latency and reactivation of M2 promoter mutants reveals significant defects. Bulk splenocytes were harvested from MHV68-infected C57BL/6J mice at day 16 and analyzed by LD analyses to determine the frequency of splenocytes harboring the viral genome and capable of spontaneously reactivating virus upon explant. (A and C) LD-PCR determination of the frequency of cells harboring the viral genome (see Materials and Methods). (B and D) LD ex vivo reactivation determination of the frequency of cells reactivating virus (see Materials and Methods). Plated in parallel, splenocytes that were mechanically disrupted allowed the presence of preformed infectious virus to be distinguish from reactivation from latency (see Materials and Methods). Notably, no preformed infectious virus was detected in these experiments (data not shown). For LD-PCR and reactivation assays, curve fit lines were derived from nonlinear regression analysis, and symbols represent mean percentages of wells positive for virus (DNA or CPE) ± the standard error of the mean. The dashed line represents 63.2%, from which the frequency of viral genome-positive cells or the frequency of cells reactivating virus was calculated based on a Poisson distribution. The data shown represent at least three independent experiments with cells pooled from five mice per experimental group.
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5861-5925 deletion mutant were nearly as impaired as the M2.Stop virus (<1 in 500,000 splenocytes reactivating virus) (Table 1 and Fig. 6B and D). The
5861-5925 deletion mutant was also significant impaired for virus reactivation (ca. 1 in 150,000 splenocytes reactivating virus versus 1 in 2,925 for wt virus) (Table 1), although when the decreased establishment of latency (ca. 13-fold) is taken into consideration, the reduction of reactivation appears to be only ca. 4-fold compared to wt virus (Table 1). This suggests that the proximal transcription initiation site may play an important role in establishment of MHV68 latency and a less prominent role in virus reactivation from latency. With respect to reactivation of the other M2 promoter mutants, as well as the M2.Stop virus, comparison of establishment of latency and reactivation cannot be as rigorously addressed because the extremely low frequency of cells reactivating virus makes it difficult to experimentally determine this frequency (reactivation frequencies for these mutants were estimated based on extrapolations of LD analyses [Fig. 6]).
M2 splice acceptor and M2 splice donor viruses exhibit defects in establishment of and reactivation from latency.
Every spliced transcript isolated in our RACE analyses contained the same splice from bp 5815 to 4609. Based on the observation that even the large M2 promoter deletion (
5861-6014) was not as impaired for establishment of latency as the M2.Stop mutant (see above), we sought to determine whether the strict use of the splice donor at bp 5814 and the splice acceptor at bp 4607 is required for efficient latency establishment and reactivation. To this end, we constructed M2 splice acceptor and M2 splice donor mutant viruses incorporating base substitutions and restriction sites that were successfully utilized in the mutagenesis of the HSV-1 genome (2) (Fig. 7A). The splice acceptor mutant incorporated an NlaIII restriction site at the acceptor, which disrupted the acceptor sequence and changed four base pairs but kept the initiation codon intact. The splice donor mutant incorporated a BanII restriction site, which disrupted the donor sequence and changed five base pairs. Two independent isolates of the M2 splice acceptor and M2 splice donor viruses were verified by Southern blotting (Fig. 7B) and DNA sequencing.
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FIG. 7. Construction of M2 splice acceptor (SA) and splice donor (SD) mutant viruses. (A) The MHV68 BAC developed by Adler et al. (1) was used to disrupt the M2 splice acceptor or splice donor sequences and incorporate an NlaIII or BanII restriction site, respectively, by RecA-mediated recombination (see Materials and Methods). The two independently generated mutants for each virus were termed M2 SA(1), M2 SA(2), M2 SD(1), and M2 SD(2). Also shown is the position for the M2 exon 2 splice acceptor site relative to the two closely spaced ATG codons, which are underlined. (B) Southern blot analyses of splice acceptor and splice donor viruses. For the splice acceptor mutants, incorporation of the NlaIII site resulted in two unique bands of 134 and 148 nt for the mutant virus isolates and a single band of 282 nt for the wt virus. For the splice donor mutants, incorporation of the BanII site resulted in two unique bands at 576 and 366 nt for the mutant virus isolates and a single band of 942 nt for the wt virus. Digests with PstI and BanII for the SA mutants or PstI and NlaIII for the SD mutants demonstrate the expected restriction pattern, demonstrating appropriate targeting of the mutation into the viral genome. Complete sequencing of the region confirmed that only the intended mutations were present (see Materials and Methods). For the SA mutant blot, the probe contained sequence from genomic coordinates bp 3822 to 5301; the probe for the SD mutant blot contained sequence from genomic coordinates bp 5090 to 6517. DNA stnds, DNA standards (100-bp ladder and 1-kb DNA ladder; New England Biolabs, Beverly, MA).
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FIG. 8. M2 splice donor and splice acceptor mutants are impaired for latency establishment and reactivation. (A) M2 splice donor and acceptor mutants replicate with wt MHV68 kinetics in an in vitro multistep growth analysis. NIH 3T12 monolayers were infected with 0.05 PFU of the indicated virus (see Materials and Methods). Error bars represent standard errors of the means from three independent experiments. (B) Frequency of cells harboring viral genome. The frequency of viral genome-positive cells was determined using an LD-PCR analysis, as described in Materials and Methods. (C) Frequency of cells reactivating virus. Serial dilutions of live, intact splenocytes were plated on MEF indicator monolayers in parallel with samples that were mechanically disrupted to distinguish between virus reactivation from latency and virus replication resulting from preformed infectious virus (see Materials and Methods). No preformed infectious virus was detected in these experiments (data not shown). For LD-PCR and reactivation assays, curve fit lines were derived from nonlinear regression analysis, and symbols represent mean percentages of wells positive for virus (DNA or CPE) ± the standard error of the mean. The dashed line represents 63.2%, from which the frequency of viral genome-positive cells or the frequency of cells reactivating virus was calculated based on a Poisson distribution. The data shown represent at least three independent experiments with cells pooled from five mice per experimental group.
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FIG. 9. Construction of M2b mutant virus. (A) The MHV68 BAC developed by Adler et al. (1) was used to introduce a translational stop codon, along with an XbaI restriction site and frameshift mutation downstream of the putative M2b initiation codon by RecA-mediated recombination (see Materials and Methods). The two independently generated isolates of this mutant virus were termed M2b.Stop(1) and M2b.Stop(2). (B) Southern blot analysis of M2b.Stop viruses. Insertion of the Stop/XbaI cassette resulted in two unique bands of 2,251 and 616 nt for the M2b.Stop viruses and a single band of 2,867 nt for the wt virus. Digestion with BamHI and EcoRI demonstrated the absence of spurious mutations, and complete sequencing of the M2 gene region confirmed that only the intended mutations were present. The probe contained sequence from MHV68 genomic coordinates bp 4652 to 6559. Molecular size markers (1-kb DNA ladder; New England Biolabs, Beverly, MA) were run in the last lane.
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FIG. 10. In vivo analysis of M2b mutant viruses. (A) Frequency of cells harboring the viral genome. The frequency of viral genome-positive cells was determined by using an LD-PCR assay. Serial dilutions of splenocytes were plated into a background of 1 x 104 uninfected cells, lysed, and analyzed with a nested PCR to detect viral genomes (see Materials and Methods). (B) Frequency of cells reactivating virus. Serial dilutions of live, intact splenocytes were plated on MEF indicator monolayers in parallel with samples that were mechanically disrupted to distinguish between virus reactivation from latency and virus replication resulting from preformed infectious virus (see Materials and Methods). No preformed infectious virus was detected in these experiments (data not shown). For LD-PCR and reactivation assays, curve fit lines were derived from nonlinear regression analysis, and symbols represent mean percentages of wells positive for virus (DNA or CPE) ± the standard error of the mean. The dashed line represents 63.2%, from which the frequency of viral genome-positive cells or the frequency of cells reactivating virus was calculated based on a Poisson distribution. The data shown represent at least three independent experiments with cells pooled from five mice per experimental group.
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With respect to M2 gene transcription, the 5' RACE analyses provide evidence that multiple, closely linked promoters are involved in driving M2 gene transcription. The observation that deletion of sequences just upstream of the proximal M2 transcription initiation site (
5861-5925) led to a greater impact on establishment of latency than reactivation from latency suggests the possibility that distinct transcription regulation of the M2 gene may be involved in the role of the M2 protein in establishment of latency versus its role in reactivation from latency. Consistent with this hypothesis, the
5925-5969 mutant, which deletes sequences upstream of the identified distal M2 transcription initiation site, exhibited a slightly milder establishment defect than the
5861-5925 deletion but a more severe reactivation defect. Of course, the difficulty with such promoter deletion analyses, particularly in the case of closely spaced promoters as proposed here, is the likely possibility of deleting cis-regulatory elements that play a role in regulating transcription from both the proximal and distal promoters. Therefore, mutating/deleting these cis elements will likely lead to complex/mixed phenotypes. Notably, computer analyses of the regions upstream of the proximal and distal M2 gene transcription initiation sites reveal the presence of several potentially interesting transcription factor binding sites (Fig. 1B). Upstream of the proximal promoter there is a candidate NF-
B binding site, along with three closely spaced Ets-2 binding sites. Upstream of the distal promoter are candidate SP-1, c-Jun, and 2 MEF-2 binding sites, reminiscent of cis-regulatory elements present in the EBV immediate-early BZLF1 promoter. Thus, the organization of candidate cis elements upstream of the distal promoter is consistent with the hypothesis that this promoter may be differentially utilized during virus reactivation from latency. Future mutagenesis studies, along with analyses of specific cellular factor binding, will be required to gain a complete understanding of how M2 gene transcription is regulating during establishment of and reactivation from latency. The analyses of M2 gene transcription presented here should provide an important framework for future studies on this important MHV68 latency-associated gene product.
We thank members of the Speck laboratory for helpful comments and discussions.
Published ahead of print on 14 May 2008. ![]()
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