Host-Cell Repair of Vaccinia Virus and of Double Stranded RNA of Encephalomyocarditis Virus

IN normal human cells DNA which has been damaged by ultraviolet radiation is repaired by excision of thymidine dimers and by repair replication. Patients suffering from xeroderma pigmentosum have a hereditary defect of the excision step and therefore their cells repair ultraviolet-induced lesions in their DNA less efficiently than do normal cells^1–4. An analogous situation has been well characterized in bacteria⁵.     

Low-Resolution Structure of Vaccinia Virus DNA Replication Machinery

Smallpox caused by the poxvirus variola virus is a highly lethal disease that marked human history and was eradicated in 1979 thanks to a worldwide mass vaccination campaign. This virus remains a significant threat for public health due to its potential use as a bioterrorism agent and requires further development of antiviral drugs. The viral genome replication machinery appears to be an ideal target, although very little is known about its structure. Vaccinia virus is the prototypic virus of the Orthopoxvirus genus and shares more than 97% amino acid sequence identity with variola virus. Here we studied four essential viral proteins of the replication machinery: the DNA polymerase E9, the processivity factor A20, the uracil-DNA glycosylase D4, and the helicase-primase D5. We present the recombinant expression and biochemical and biophysical characterizations of these proteins and the complexes they form. We show that the A20D4 polymerase cofactor binds to E9 with high affinity, leading to the formation of the A20D4E9 holoenzyme. Small-angle X-ray scattering yielded envelopes for E9, A20D4, and A20D4E9. They showed the elongated shape of the A20D4 cofactor, leading to a 150-Å separation between the polymerase active site of E9 and the DNA-binding site of D4. Electron microscopy showed a 6-fold rotational symmetry of the helicase-primase D5, as observed for other SF3 helicases. These results favor a rolling-circle mechanism of vaccinia virus genome replication similar to the one suggested for tailed bacteriophages.     

Cellular Autophagy Machinery is not Required for Vaccinia Virus Replication and Maturation

The origin of the primary membrane of vaccinia virus, the double-membrane structure that surrounds the immature virions (IV), is not fully understood. Here we investigated whether the primary membrane is of autophagy origin. Morphologic studies by electron microscopy showed no apparent difference in viral maturation in the autophagy deficient cell lines, the Atg5-/- mouse embryonic fibroblast (MEF) and the Beclin 1 -/- embryonic stem (ES) cells, compared to their isogenic wild-type counterparts. Moreover, quantitative assays indicated that the viruses replicate and maturate in the autophagy deficient cell lines as efficiently as they do in the corresponding isogenic wild type cells. This study indicates that the cellular autophagy machinery is not required for the life-cycle of vaccinia virus, suggesting that the primary vaccinia viral membrane likely does not originate from the autophagic membrane.     

The Nucleoside Triphosphatase and Helicase Activities of Vaccinia Virus NPH-II Are Essential for Virus Replication

Vaccinia virus NPH-II is the prototypal RNA helicase of the DExH box protein family, which is defined by six shared sequence motifs. The contributions of conserved amino acids in motifs I (TGVGKTSQ), Ia (PRI), II (DExHE), and III (TAT) to enzyme activity were assessed by alanine scanning. NPH-II-Ala proteins were expressed in baculovirus-infected Sf9 cells, purified, and characterized with respect to their RNA helicase, nucleic acid-dependent ATPase, and RNA binding functions. Alanine substitutions at Lys-191 and Thr-192 (motif I), Arg-229 (motif Ia), and Glu-300 (motif II) caused severe defects in RNA unwinding that correlated with reduced rates of ATP hydrolysis. In contrast, alanine mutations at His-299 (motif II) and at Thr-326 and Thr-328 (motif III) elicited defects in RNA unwinding but spared the ATPase. None of the mutations analyzed affected the binding of NPH-II to RNA. These findings, together with previous mutational studies, indicate that NPH-II motifs I, Ia, II, and VI (QRxGRxGRxxxG) are essential for nucleoside triphosphate (NTP) hydrolysis, whereas motif III and the His moiety of the DExH-box serve to couple the NTPase and helicase activities. Wild-type and mutant NPH-II-Ala genes were tested for the ability to rescue temperature-sensitive nph2-ts viruses. NPH-II mutations that inactivated the phosphohydrolase in vitro were lethal in vivo, as judged by the failure to recover rescued viruses containing the Ala substitution. The NTPase activity was necessary, but not sufficient, to sustain virus replication, insofar as mutants for which NTPase was uncoupled from unwinding (H299A, T326A, and T328A) were also lethal. We conclude that the phosphohydrolase and helicase activities of NPH-II are essential for virus replication.     

Vaccinia Virus DNA Replication Occurs in Endoplasmic Reticulum-enclosed Cytoplasmic Mini-Nuclei

Vaccinia virus (vv), a member of the poxvirus family, is unique among most DNA viruses in that its replication occurs in the cytoplasm of the infected host cell. Although this viral process is known to occur in distinct cytoplasmic sites, little is known about its organization and in particular its relation with cellular membranes. The present study shows by electron microscopy (EM) that soon after initial vv DNA synthesis at 2 h postinfection, the sites become entirely surrounded by membranes of the endoplasmic reticulum (ER). Complete wrapping requires ~45 min and persists until virion assembly is initiated at 6 h postinfection, and the ER dissociates from the replication sites. [(3)H]Thymidine incorporation at different infection times shows that efficient vv DNA synthesis coincides with complete ER wrapping, suggesting that the ER facilitates viral replication. Proteins known to be associated with the nuclear envelope in interphase cells are not targeted to these DNA-surrounding ER membranes, ruling out a role for these molecules in the wrapping process. By random green fluorescent protein-tagging of vv early genes of unknown function with a putative transmembrane domain, a novel vv protein, the gene product of E8R, was identified that is targeted to the ER around the DNA sites. Antibodies raised against this vv early membrane protein showed, by immunofluorescence microscopy, a characteristic ring-like pattern around the replication site. By electron microscopy quantitation the protein concentrated in the ER surrounding the DNA site and was preferentially targeted to membrane facing the inside of this site. These combined data are discussed in relation to nuclear envelope assembly/disassembly as it occurs during the cell cycle.     

Irreversible Effects of Cycloheximide During the Early Period of Vaccinia Virus Replication

The presence of cycloheximide, an inhibitor of protein synthesis, during the period 30 to 60 min after vaccinia infection produced an irreversible block in virus replication. In contrast (i) cycloheximide given at earlier or later times, even for prolonged periods, did not prevent continuation of the infectious cycle after removal of the drug, and (ii) treatment with cycloheximide during the first 2 hr did not prevent virus growth when the early stages of replication proceeded more slowly due to infection with a low multiplicity of virus. These findings were interpreted as an indication that protein synthesis is required at a critical time in the virus growth cycle. Under the conditions in which brief cycloheximide treatment prevented virus growth, ribonucleic acid (RNA) synthesis continued at an undiminished rate for at least 2 hr after removal of the drug. Although this RNA appeared identical by polyacrylamide gel electrophoresis to "early" viral messenger RNA, it was not found associated with ribosomes or polyribosomes. Failure to observe viral protein synthesis was consistent with the latter finding. It appeared unlikely that the translational block resulted from inadequate removal of cycloheximide, since the effects of the drug were shown to be reversible at earlier or later times in infection or even at the same time when a lower multiplicity of virus was used. Interference with the normal synthesis of specific viral protein factors required for translation was postulated to explain the results.     

Sequential Formation of Vaccinia Virus Proteins and Viral Deoxyribonucleic Acid Replication

In vaccinia virus-infected cell cultures, cellular protein synthesis was inhibited 50% at 2 hr postinfection (PI) and 80 to 90% by 4 hr PI. Input virus was responsible for this inhibition. Five early proteins, coded for by the viral genome, could be detected at 2 to 3 hr PI. Normally, their synthesis did not continue beyond 6 hr PI, at which time synthesis of a different set of proteins began. When DNA replication was blocked, synthesis of these early proteins continued until 9 to 12 hr PI. The bulk of the proteins which were incorporated into mature virus were synthesized at 8 hr PI and thereafter. The time of their formation was close to the time at which virus maturation occurred. However, 15% of the protein found in mature virus was synthesized early in the infectious cycle. The quantity of “early viral protein” which was not incorporated into mature virus was almost as large as the quantity of viral protein which did appear in mature virus. The “early” and “late” proteins could be shown to have separate and distinct immunological properties. The role of this large quantity of “early” protein is discussed.     

Mechanism of Inhibition of Vaccinia Virus Replication in Adenovirus-Infected HeLa Cells

The ability of vaccinia virus to replicate in HeLa cells which had been previously infected with adenovirus type 2 (Ad2) was studied in order to gain insight into the mechanism by which adenovirus inhibits the expression of host cell functions. Vaccinia virus was employed in these studies because it replicates in the cytoplasm, whereas Ad2 replicates in the nucleus of the cell. It was found that vaccinia deoxyribonucleic acid (DNA) synthesis is greatly inhibited in adeno-preinfected HeLa cells provided that vaccinia superinfection does not occur before 18 hr after adeno infection. The inhibition of vaccinia DNA synthesis can be traced to an inhibition of vaccinia protein synthesis and viral uncoating. Vaccinia ribonucleic acid (RNA) synthesis is not inhibited in adeno-preinfected cells, but the vaccinia RNA does not become associated with polysomes.     

Cidofovir Inhibits Genome Encapsidation and Affects Morphogenesis during the Replication of Vaccinia Virus

Cidofovir (CDV) is one of the most effective antiorthopoxvirus drugs, and it is widely accepted that viral DNA replication is the main target of its activity. In the present study, we report a detailed analysis of CDV effects on the replicative cycles of distinct vaccinia virus (VACV) strains: Cantagalo virus, VACV-IOC, and VACV-WR. We show that despite the approximately 90% inhibition of production of virus progeny, virus DNA accumulation was reduced only 30%, and late gene expression and genome resolution were unaltered. The level of proteolytic cleavage of the major core proteins was diminished in CDV-treated cells. Electron microscopic analysis of virus-infected cells in the presence of CDV revealed reductions as great as 3.5-fold in the number of mature forms of virus particles, along with a 3.2-fold increase in the number of spherical immature particles. A detailed analysis of purified virions recovered from CDV-treated cells demonstrated the accumulation of unprocessed p4a and p4b and nearly 67% inhibition of DNA encapsidation. However, these effects of CDV on virus morphogenesis resulted from a primary effect on virus DNA synthesis, which led to later defects in genome encapsidation and virus assembly. Analysis of virus DNA by atomic force microscopy revealed that viral cytoplasmic DNA synthesized in the presence of CDV had an altered structure, forming aggregates with increased strand overlapping not observed in the absence of the drug. These aberrant DNA aggregations were not encapsidated into virus particles.Vaccinia virus (VACV) is the prototypical member of the Poxviridae, a family of large DNA-containing viruses. During infection, a cascade of temporally regulated viral gene expression occurs exclusively in the cell cytoplasm, where viral DNA replication takes place. DNA replication is essential for the onset of the intermediate and late steps of viral gene expression (37). VACV morphogenesis is a complex process that starts within the virus factories, or virosomes, in parallel with the late stage of gene expression. Crescent-shaped virus membranes evolve into immature spherical particles (IV) that subsequently progress to form brick-shaped mature virions (MV) (reviewed in reference 8). Virus assembly and maturation are complex processes requiring telomere resolution of newly replicated DNA (20, 36, 40), genome encapsidation (6, 22, 50), and the proteolytic processing of major structural proteins (38, 51). For the past decade, several reports have analyzed in detail these numerous steps of VACV morphogenesis, unraveling the role of distinct virus late proteins in the progression of viral particle formation (reviewed in reference 8).Cantagalo virus (CTGV) is a strain of VACV isolated from pustular lesions on cows in Brazil (10). Similar outbreaks of vaccinia-like viruses have been reported frequently over the past 8 years (14, 39, 48). Interestingly, the majority of these vaccinia viruses circulating in the wild in Brazil bear a striking similarity to the Brazilian vaccine strain used for systematic vaccination during the eradication campaign, which was produced in Rio de Janeiro (19) and called strain IOC (10). This similarity raises the interesting possibility that the circulating vaccinia viruses represent feral derivatives of IOC or of a closely related ancestor. Little is known about the sensitivity of these novel vaccinia viruses to antiviral compounds. In the absence of an active smallpox vaccination campaign, the spread of these vaccinia viruses in the wild, the prevalence of cowpox infections in Europe and elsewhere (39), and the occurrence of complications from smallpox vaccination (52) make the need for effective antipoxvirus treatment a worldwide concern.Cidofovir (CDV), an acyclic pyrimidine phosphonate analogue, has shown a potent antiviral effect on several poxvirus infections (4, 15, 44, 46). Recently, we have reported the efficacy of CDV in inhibiting the replication of the Brazilian VACV strains CTGV and IOC (26). The mechanism of action of CDV on reactions catalyzed by the VACV DNA polymerase has been studied in vitro. CDV is not a chain-terminating analogue but drastically slows chain extension and inhibits the 3′-5′ exonuclease proofreading activity of the enzyme (34). In addition, templates containing CDV cause inhibition of DNA elongation (33). Differences between the effects of CDV on human cytomegalovirus (55) and VACV enzymes have been observed, but overall it has been widely accepted that CDV acts by inhibiting the process of virus DNA replication. Moreover, most CDV-resistant VACV strains contain mutations in the catalytic domain or in the 3′-5′ exonuclease domain of the DNA polymerase (2, 5, 28, 45).Despite the consensus regarding mechanisms of action, the effects of CDV on the stages of the VACV replicative cycle have never been analyzed. We report here that although CDV led to approximately 90% inhibition of VACV progeny production, we observed only 30% inhibition of DNA replication and normal levels of postreplicative virus gene expression. However, the encapsidation of DNA into virus particles and the proteolytic processing of the major core proteins were inhibited in CDV-treated cells, leading to an impairment of virus morphogenesis. These effects on virus assembly are an indirect result of a primary effect of CDV on VACV DNA synthesis. Atomic force microscopy (AFM) analysis revealed that virus DNA isolated from the cytoplasm of CDV-treated cells formed aggregates of highly entangled and intertwined DNA molecules that were not observed in cytoplasmic viral DNA isolated from untreated cells. In addition, these DNA aggregates were not detected in encapsidated virus genomes isolated from particles purified from untreated or CDV-treated cells. Our data suggest that incorporation of CDV into VACV DNA during the replication process may lead to aberrant DNA structures, which are less able to be packaged into virus particles.     

Differential RNA Sequence Requirement for Dengue Virus Replication in Mosquito and Mammalian Cells

Dengue virus cycles between mosquitoes and humans. Each host provides a different environment for viral replication, imposing different selective pressures. We identified a sequence in the dengue virus genome that is essential for viral replication in mosquito cells but not in mammalian cells. This sequence is located at the viral 3′ untranslated region and folds into a small hairpin structure. A systematic mutational analysis using dengue virus infectious clones and reporter viruses allowed the determination of two putative functions in this cis-acting RNA motif, one linked to the structure and the other linked to the nucleotide sequence. We found that single substitutions that did not alter the hairpin structure did not affect dengue virus replication in mammalian cells but abolished replication in mosquito cells. This is the first sequence identified in a flavivirus genome that is exclusively required for viral replication in insect cells.     

Vaccinia Virus Replication and Cytopathic Effect in Cultures of Phytohemagglutinin-treated Human Peripheral Blood Leukocytes

Titers of vaccinia virus consistently increased in cultures of washed phytohemagglutinin-treated, peripheral blood leukocytes of a vaccinated adult. Concomitantly, a gradual rise occurred in the numbers of infected leukocytes, as determined by the infective center assay. Increase in viral titer was accompanied by cell injury, decline in cell numbers, and decreased acid production. Leukocytes not pretreated with phytohemagglutinin appeared to form infective centers after exposure to the vaccinia agent, but they did not replicate infectious virus. For viral replication, the continuous presence of phytohemagglutinin was required.     

The Vaccinia Virus Superoxide Dismutase-Like Protein (A45R) Is a Virion Component That Is Nonessential for Virus Replication

A characterization of the A45R gene from vaccinia virus (VV) strain Western Reserve is presented. The open reading frame is predicted to encode a 125-amino-acid protein (M(r), of 13,600) with 39% amino acid identity to copper-zinc superoxide dismutase (Cu-Zn SOD). Sequencing of the A45R gene from other orthopoxviruses, here and by others, showed that the protein is highly conserved in all viruses sequenced, including 16 strains of VV, 2 strains of cowpox virus, camelpox virus, and 4 strains of variola virus. In all cases the protein lacks key residues involved in metal ion binding that are important for the catalytic activity. The A45R protein was expressed in Escherichia coli, purified, and tested for SOD activity, but neither enzymatic nor inhibitory SOD activity was detected. Additionally, no virus-encoded SOD activity was detected in infected cells or purified virions. A monoclonal antibody raised against the A45R protein expressed in E. coli identified the A45R gene product as a 13.5-kDa protein that is expressed late during VV infection. Confocal microscopy of VV-infected cells indicated that the A45R protein accumulated predominantly in cytoplasmic viral factories. Electron microscopy and biochemical analyses showed that the A45R protein is incorporated into the virion core. A deletion mutant lacking the majority of the A45R gene and a revertant virus in which the deleted gene was restored were constructed and characterized. The growth properties of the deletion mutant virus were indistinguishable from those of wild-type and revertant viruses in all cell lines tested, including macrophages. Additionally, the virulence and pathogenicity of the three viruses were also comparable in murine and rabbit models of infection. A45R is unusual in being the first VV core protein described that affects neither virus replication nor virulence.