Origin-independent plasmid replication occurs in vaccinia virus cytoplasmic factories and requires all five known poxvirus replication factors
© De Silva and Moss. 2005
Received: 10 March 2005
Accepted: 22 March 2005
Published: 22 March 2005
Replication of the vaccinia virus genome occurs in cytoplasmic factory areas and is dependent on the virus-encoded DNA polymerase and at least four additional viral proteins. DNA synthesis appears to start near the ends of the genome, but specific origin sequences have not been defined. Surprisingly, transfected circular DNA lacking specific viral sequences is also replicated in poxvirus-infected cells. Origin-independent plasmid replication depends on the viral DNA polymerase, but neither the number of additional viral proteins nor the site of replication has been determined.
Using a novel real-time polymerase chain reaction assay, we detected a >400-fold increase in newly replicated plasmid in cells infected with vaccinia virus. Studies with conditional lethal mutants of vaccinia virus indicated that each of the five proteins known to be required for viral genome replication was also required for plasmid replication. The intracellular site of replication was determined using a plasmid containing 256 repeats of the Escherichia coli lac operator and staining with an E. coli lac repressor-maltose binding fusion protein followed by an antibody to the maltose binding protein. The lac operator plasmid was localized in cytoplasmic viral factories delineated by DNA staining and binding of antibody to the viral uracil DNA glycosylase, an essential replication protein. In addition, replication of the lac operator plasmid was visualized continuously in living cells infected with a recombinant vaccinia virus that expresses the lac repressor fused to enhanced green fluorescent protein. Discrete cytoplasmic fluorescence was detected in cytoplasmic juxtanuclear sites at 6 h after infection and the area and intensity of fluorescence increased over the next several hours.
Replication of a circular plasmid lacking specific poxvirus DNA sequences mimics viral genome replication by occurring in cytoplasmic viral factories and requiring all five known viral replication proteins. Therefore, small plasmids may be used as surrogates for the large poxvirus genome to study trans-acting factors and mechanism of viral DNA replication.
Vaccinia virus (VAC), the prototype for the family Poxviridae, is a large double-stranded DNA virus that encodes numerous enzymes and factors needed for RNA and DNA synthesis, enabling it to replicate in the cytoplasm of infected cells . More than 20 viral proteins including a multi-subunit RNA polymerase and stage specific transcription factors are involved in viral RNA synthesis . Genetic and biochemical studies identified five viral proteins essential for viral DNA replication, namely the viral DNA polymerase [3–8], polymerase processivity factor [9, 10], DNA-independent nucleoside triphosphatase [11–13], serine/threonine protein kinase [14–17], and uracil DNA glycosylase [18–21]. In addition, the virus encoded Holliday junction endonuclease is required for the resolution of DNA concatemers into unit-length genomes . Other proteins that may contribute to viral DNA replication, include DNA type I topoisomerase, single stranded DNA binding protein, DNA ligase, thymidine kinase, thymidylate kinase, ribonucleotide reductase and dUTPase (reviewed in reference ).
The VAC genome consists of a 192 kbp linear duplex DNA with covalently closed hairpin termini [23, 24]. A model for poxvirus DNA replication begins with the introduction of a nick near one or both ends of the hairpin termini, followed by polymerization of nucleotides at the free 3'-OH end, strand displacement and concatemer resolution [25, 26]. Nicking is supported by changes in the sedimentation of the parental DNA following infection, and labeling studies suggested that replication begins near the ends of the genome [27, 28]. Efforts to locate a specific origin of replication in the VAC genome led to the surprising conclusion that any circular DNA replicated as head-to-tail tandem arrays in cells infected with VAC [29, 30]. Origin-independent plasmid replication was also shown to occur in the cytoplasm of cells infected with other poxviruses including Shope fibroma virus and myxoma virus as well as with African swine fever virus [30, 31]. In contrast, studies with linear minichromosomes containing hairpin termini provided evidence for cis-acting elements in VAC DNA replication . It was considered that plasmid replication might be initiating non-specifically, perhaps at random nicks in DNA.
Although transfected plasmids were used to study the resolution of poxvirus concatemer junctions [33–37], the system has not been exploited for studies of viral DNA synthesis. The goal of the present study was to determine how closely plasmid replication mimics viral genome replication. For example, if some viral proteins are needed for initiating DNA synthesis at specific origins near the ends of the viral genome, they might not be required for plasmid replication. In addition, we were curious as to whether synthesis of plasmid DNA occurs diffusely in the cytoplasm, since the transfected DNA enters cells independently of virus and contains no viral targeting sequences. Contrary to these speculations, we found that each of the five viral proteins known to be required for viral genome replication was needed for origin-independent replication of plasmids. Moreover, both plasmid and genome replication occurred in discrete viral cytoplasmic factory areas. Thus, small circular plasmids are useful surrogates for the large viral genome in studying the mechanism of poxvirus DNA replication and the trans-acting factors required.
Determination of plasmid replication by real-time PCR
To improve quantification of plasmid replication and to establish a non-radioactive method for rapid analysis of multiple samples, we devised a real-time PCR assay using primers 152 bp apart that flanked two DpnI/MboI sites in a circular plasmid lacking VAC DNA sequences. In initial experiments, we followed the protocol of previous studies by transfecting the plasmid after infection [29, 30]. However, MboI-resistant input DNA as well as DpnI-resistant replicated DNA increased with time, suggesting that entry of DNA into the cell occurred continuously even though the medium was changed at 4 h (data not shown). To avoid this problem in subsequent experiments, DNA was transfected 24 h prior to infection. Total DNA was isolated at various times, digested with DpnI, MboI, or left uncut and subjected to real-time PCR. Under these conditions, MboI-resistant DNA did not increase, whereas DpnI-resistant DNA increased ~18 fold between 3 and 6 h and ~400 fold by 24 h (Fig. 1B). Moreover, total DNA increased ~10 fold. Increased DpnI-resistant DNA was not detected in mock-infected cells (data not shown).
Previous Southern blotting studies had indicated that plasmid replication paralleled genome replication . We compared the kinetics of plasmid replication obtained by real-time PCR with Southern blotting. For the latter analysis, total DNA was first digested with EcoRI to resolve head-to-tail concatemers into linear units followed by digestion with MboI or DpnI. After electrophoresis, the DNA was transferred to a nylon membrane, hybridized to a 32P-labeled plasmid probe, and the amount of DNA quantified using a PhosphorImager. The DpnI-resistant and total DNA increased with time, whereas the MboI-resistant DNA did not (Fig. 1C). The Southern blot analysis suggested that the amount of replicated plasmid plateaued after 12 h, whereas it continued to increase slightly as determined by PCR (Fig. 1B), suggesting that the latter method has the greater dynamic range as well as being more convenient.
Determination of the trans-acting factors required for plasmid replication
Previous studies had shown that expression of VAC uracil DNA glycosylase was required for genome replication . To determine whether this protein is required for plasmid replication, we used mutant virus vD4-ZG, in which the uracil DNA glycosylase gene was deleted , and rabbit cell lines lacking (RK-13) or stably expressing (RKD4R) VAC uracil DNA glycosylase . We found that plasmid DNA replication was only detected in the cell line stably expressing the viral uracil DNA glycosylase (Fig. 2B), indicating a requirement for this protein as well as each of the other four factors.
Transfected plasmid DNA accumulates in viral factories
Visualization of replicating plasmid DNA in live cells
The replication of circular DNA lacking viral sequences as head-to-tail concatemers in the cytoplasm of cells infected with a poxvirus was reported nearly 20 years ago [29, 30]. Fortuitous poxviral origins were ruled out by the replication of 5 different circular DNAs and no evidence was obtained for integration into the viral genome by non-homologous recombination. These data strongly suggested autonomous plasmid replication by a rolling circle or theta mechanism. The significance of sequence non-specific DNA replication was called into question by Du and Traktman , who reported only low-level replication of a super coiled plasmid compared to a linear minichromosome containing specific telomere sequences . However, our determination of a 10-fold increase in net plasmid DNA compares favorably to the 2-fold increase achieved with the most efficient minichromosome construct . Moreover, our finding was similar to the 8-fold increase in net plasmid DNA reported by DeLange and McFadden . There are several procedural differences that might account for the disparate results. One difference was the type of virus and cell used: Du and Traktman used mouse L cells infected with VAC, DeLange and McFadden principally used rabbit cells infected with myxoma virus or Shope fibroma virus and we used monkey or HeLa cells infected with VAC. A second difference was the method of DNA isolation. Whereas we and DeLange and McFadden proteinase digested whole cell lysates, Du and Traktman lysed cells with cold hypotonic buffer containing a non-ionic detergent and removed nuclei by sedimentation prior to DNA extraction. VAC DNA replication occurs in juxtanuclear factories and loss of high molecular weight protein-DNA complexes, especially those containing long head-to-tail plasmid DNA concatemers upon centrifugation is a concern. Indeed, Du and Traktman  reported that the presence of the telomere resolution sequence was required for high efficiency replication of linear minichromosomes and that only monomeric products were recovered. Further studies are needed to determine whether the cis-acting sequences in the linear minichromosomes are serving as origins of replication or as concatemer resolution sites or both.
The temporal coincidence of plasmid and viral DNA replication suggested that viral proteins were needed for each. Indeed, we found that each of the five trans-acting viral proteins known to be important for viral genome replication was similarly required for plasmid replication. Either none of these proteins have a sequence-specific role or some have dual roles and are also required for origin-independent replication. The proteins also may have structural roles in assembling the replication complex, the existence of which is suggested by the interaction of A20 with the D4 and D5 proteins  and the co-purification of the A20, D4 and E9 proteins with a processive form of DNA polymerase [46, 47].
VAC cores containing genomic DNA and an early transcription system travel from the cell entry site along microtubules to the juxtanuclear area where synthesis of early viral proteins and DNA replication result in the formation of discrete factories . It is believed that each factory arises from a single infectious particle . It was interesting to determine whether plasmid replication occurred in factories or dispersed throughout the cell. To investigate this, we transfected cells with a plasmid containing multiple repeats of the E. coli lacO, which tightly binds lacI. In one approach, the lacO DNA was located in discrete juxtanuclear regions by staining fixed and permeabilized cells with an MBP-lacI fusion protein followed by an antibody to MBP. The regions were identified as viral factories by Hoechst DNA staining and localization of the viral uracil DNA glycosylase, a protein required for replication of both plasmid and viral DNA. LacO DNA was not detected in the nucleus or in diffuse areas of the cytoplasm. A second approach involved the construction of a recombinant VAC that expresses a GFP-lacI fusion protein with a NLS to remove unbound protein from the cytoplasm. Again, the lacO DNA was found in viral factories identified with Hoechst staining and viral RNA polymerase antibody. The data suggest that for plasmid replication to occur, the DNA must be at the right place i.e. a site containing viral replication proteins. Presumably the plasmid diffuses into the factory region and is captured by DNA binding proteins. By taking time lapse images of live cells, plasmid DNA was detected in juxtanuclear sites at 6 to 7 h after infection and increased in intensity as the factories enlarged over the next several hours. Factory enlargement appeared to occur from within rather than by fusion of multiple small factories. We suspect that the latter might occur if higher multiplicities of virus were used.
In contrast to the cytoplasmic replication of genome and plasmid DNA in VAC-infected cells, Sourvinos et al.  visualized nuclear replication of herpes simplex virus amplicons containing tetracycline operator sequence and Fraefel et al.  incorporated lacO sites into the genome of adenovirus associated virus and visualized discrete replication sites in the nucleus that fused to form larger structures. The latter study encouraged us to try to incorporate long tandem arrays of lacO repeats in the VAC genome, but they were unstable.
We described a sensitive and quantitative real-time PCR method of measuring plasmid replication in cells infected with VAC and demonstrated that origin-independent replication requires all known viral replication proteins. In addition, we visualized the plasmid in living and fixed cells by incorporating tandem lacO sequences and determined that replication occurred in cytoplasmic viral factories. This system should be useful for studying the mechanism and minimal requirements of poxvirus DNA replication.
Cells, plasmids, and viruses
RK-13, BS-C-1, BS-C-40, HuTK- 143B, and HeLa cells were maintained in Eagle's minimal essential medium (EMEM; Quality Biologicals, Inc. Gaithersburg, MD) or Dulbecco's modified Eagle's medium (DMEM; Quality Biologicals, Inc.) containing 10% fetal bovine serum (FBS). A rabbit kidney cell line (RKD4R) stably expressing the VAC uracil DNA glycosylase and recombinant VAC vD4-ZG lacking a functional D4R gene  were gifts of F.G. Falkner. Plasmid pSV9 contains two copies of a 2.6 kbp insert derived from the VAC concatemer junction and two copies of pUC13 DNA . Linear minichromosomes containing 1.3 kbp of VAC telomere sequences were prepared by ligation of snap cooled, EcoRI digested pSV9 essentially as described by Du and Traktman . Ligation resulted in three products of 8 kbp, 2.6 kbp and 5.3 kbp. The 5.3 kbp minichromosome fragment was isolated by gel electrophoresis and the Qiaex II gel extraction kit (Qiagen). Plasmid p716  was kindly provided by A. McBride; plasmids pSV2-dhfr-8.32 and p3'SS dimer-Cl-EGFP  were gifts of A. Belmont. The temperature sensitive (ts) replication mutants Cts16, Cts24, Cts42, Cts25 with mutations in the I7, D5, E9 and B1 open reading frames, respectively were obtained from R. Condit [53, 54]; mut185 has a ts mutation in the A20 ORF .
Cy5-conjugated affinipure F(ab')2 fragment of donkey anti-mouse IgG and Texas red dye conjugated affinipure F(ab')2 of donkey anti-rabbit IgG were obtained from Jackson ImmunoResearch laboratories. Alexa Fluor 594 goat anti-rabbit IgG was from Molecular probes. New England Biolabs and Invitrogen supplied the rabbit antibody to MBP and mouse anti-V5 monoclonal antibody, respectively.
Transfection, infection and isolation of DNA
For experiments analyzed by real-time PCR, 0.1 μg of p716 DNA and 3.9 μg of salmon sperm carrier DNA were mixed with 10 μg of lipofectamine 2000 (Invitrogen) and uninfected cells were transfected according to the manufacturer's instructions. After 24 h, the cells were infected with VAC strain WR, vD4-ZG or a ts mutant at a multiplicity of 3 PFU per cell. Cells were then washed twice with Opti-MEM (Invitrogen) and overlaid with EMEM with 2.5% FBS. At various times, cells were harvested and the DNA isolated using the Qiamp DNA Blood Kit (Qiagen) according to the manufacturer's instructions. DNA was digested with restriction enzymes DpnI or MboI (New England Biolabs).
DNA (2 μg) was digested with EcoRI and DpnI or MboI, resolved on a 0.8% agarose gel, and transferred to Immobilon-Ny+ (Millipore) transfer membrane. Southern blotting was carried out as described by Maniatis . Plasmid DNA was detected with a DNA probe that was 32P-labeled using a random-priming kit (Invitrogen). Pre-hybridizations and hybridizations were carried out using Quik-Hyb (Stratagene) according to the manufacturer's recommendation. The blot was exposed to a Phosphor screen and data acquired on a Storm 860 PhosphoImager (Molecular Dynamics, Sunnyvale, CA) and quantified with ImageQuant software (Molecular Dynamics).
Oligonucleotides P1 (5'CAACTAAATGTGCAAGCAATGTAATTC3') and P2 (5'CATCCTGCCCCTTGCTGT3') were designed with Primer Express software supplied by Applied Biosystems. Reactions were carried out using SYBR Green PCR master mix (Applied Biosystems), 10 μM of each primer, and 1 ng of DNA in a total volume of 50 μl in an Applied Biosystems Prism 7900HT sequence detection system with v2.1.1 software. For amplification 40 cycles at 95°C for 15 s and 60°C for 60 s were used.
Construction of recombinant viruses
vGFP-lacI: the open reading frame that encodes GFP-lacI was cloned by PCR using primers 5'CAGGCTGCGCAACTGTTGGGAAGGGCGA3' and 5'AAAAGTACTAGCCTGGGGTGCCTAATGAGTGAGC3' with p3'SS dimer-Cl-EGFP  as a template. The PCR product was digested with XhoI and ScaI and then ligated to XhoI and StuI digested pSC59  to form the plasmid pSC59gfplacI. BS-C-1 cells were infected with VAC strain WR at 0.05 PFU per cell for 1 h and then transfected with 2 μg pSC59gfplacI using 10 μg of Lipofectamine 2000. After 5 h, the medium was replaced with EMEM plus 2.5% FBS and the incubation continued for 2 days. Cells were harvested and lysed, and the diluted lysates were used to infect HuTK- 143B cell monolayers. The cells were overlaid with medium containing low melting point agarose and 25 μg of 5-bromodeoxyuridine per ml. After three rounds of plaque purification, the viral DNA was screened for the presence of the inserted DNA by PCR. The recombinant virus was propagated and titrated as described previously . vV5D4: primers 5'ACTAGATACGTATAAAAAGGTATCTAATTTGATATAATGGGTAAGCCTATCCCTAACCCTCTCCTCGGTCTCGATTCTACGAATTCAGTGACTGT3' and 5'CTCCTGGACGTAGCCTTCGGG3' and DNA from plasmid pER-GFP  were used to add a V5 tag to the VAC D4R gene. After double digestion of the PCR product and plasmid with SnaBI and SmaI, the products were ligated together to form the new plasmid pERV5-GFP. Approximately 106 RKD4R cells were infected with vD4-ZG at a multiplicity of 0.05 PFU per cell for 1 h at 37°C. The infected cells were washed twice with Opti-MEM and transfected with 2 μg of pERV5-GFP using 10 μg of Lipofectamine 2000. After 5 h, the transfection mixture was replaced with EMEM containing 2.5% FBS, and the cells were harvested at 48 h in 0.5 ml of EMEM-2.5% FBS. Lysates were prepared by freezing and thawing the cells three times and sonicating them twice for 30 s. Recombinant viruses that expressed GFP were plaque purified five times on RKD4R cells. The genetic purity of recombinant viruses was confirmed by PCR and sequencing. The recombinant virus was propagated and titrated as described previously .
Construction and expression of MBP-lacI
The lac repressor gene was PCR amplified using the following primers 5'CGGAATTCTCATCGGGAAACCTGTCGTGCCAGCTGC3' and 5'CGCGGATCCTAGTGAAACCAGTAACGTTATACG3' and template DNA from p3'SS dimer-Cl-EGFP. The amplified fragment was cloned into the BamHI and EcoRI sites of the expression vector pMal-c2x (New England Biolabs) resulting in the plasmid pMalc2x-lacI. Luria-Bertani medium (500 ml) supplemented with ampicillin (100 μg/ml) and glucose (0.2% w/v) was inoculated with 5 ml of an overnight culture of the E. coli ER2507 (New England Biolabs) containing the recombinant pMalc2x-lacI plasmid. The culture was grown at 37°C to a cell density of 0.5 at A600 nm and the expression of protein was induced for 2 h at 37°C by adding isopropyl-β-D-thiogalactopyranoside to a final concentration of 0.3 mM. The culture was then centrifuged at 4000 × g for 20 min at 4°C. A cell extract was prepared using B-PER reagent (Pierce) according to the manufacturer's recommendation and the protein purified using the pMAL protein fusion and purification kit (New England Biolabs).
Confocal microscopy and live cell imaging
Cells were plated on glass cover slips in 12 well plates and transfected with 1 μg of pSV2-dhfr-8.32 using 5 μg of Lipofectamine 2000. After 24 h, cells were infected with recombinant VAC at 3 PFU per cell. At 12 h after infection, cells were fixed with cold 4% paraformaldehyde in phosphate buffered saline (PBS) at room temperature for 20 min. Fixed cells were permeabilized for 5 min with PBS containing either 0.2% Triton X-100 at room temperature. Permeabilized cells were incubated with primary antibodies at a 1:100 dilution in10% FBS for 30 min, washed with PBS three times, and then incubated with secondary antibody at a 1:100 dilution in 10% FBS for 30 min at room temperature. After washing with PBS three times, cover slips were incubated with Hoechst dye for 10 min at room temperature to visualize DNA staining. Stained cells were washed extensively with PBS and cover slips mounted in 20% glycerol. Cellular fluorescence was examined under a Leica TCS NT inverted confocal microscope and images were overlaid using Adobe Photoshop version 5.0.2.
For live cell imaging, HeLa cells were plated at ~80% confluence onto TC3 dishes (Bioptechs, Inc.) and infected with 3 PFU of virus per cell on the next day. Cells were imaged by either confocal or video microscopy. For video microscopy, a Hammumatsu C5985 camera and controller were attached to a Leica DMIRBE inverted fluorescence microscope. Images were digitized using an IC-PCI video capture card (Coreco Imaging, Inc.) controlled by Image Pro Plus software. Cells were maintained on a heated TC3 stage (Bioptechs, Inc.) with the temperature set at 37°C.
We thank Norman Cooper for invaluable assistance with cell culture, Owen Schwartz for helping in confocal microscopy and live cell imaging, and Mike Baxter for his assistance in real-time PCR. A. McBride and A. Belmont provided plasmids and R. Condit and F. Falkner donated mutant viruses and a cell line.
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