Genetic and phylogenetic characterization of the type II cyclobutane pyrimidine dimer photolyases encoded by Leporipoxviruses.

Shope fibroma virus and myxoma virus encode proteins predicted to be Type II photolyases. These are enzymes that catalyze light-dependent repair of cyclobutane pyrimidine dimers (CPDs). When the Shope fibroma virus S127L gene was expressed in an Escherichia coli strain lacking functional CPD repair pathways, the expressed gene protected the bacteria from 70-75% of the ultraviolet (UV) light-induced cytotoxic DNA damage. This proportion suggests that Leporipoxvirus photolyases can only repair CPDs, which typically comprise approximately 70% of the damage caused by short wavelength UV light. To test whether these enzymes can protect virus genomes from UV, we exposed virus suspensions to UV-C light followed by graded exposure to filtered visible light. Viruses encoding a deletion of the putative photolyase gene were unable to photoreactivate UV damage while this treatment again eliminated 70-90% of the lethal photoproducts in wild-type viruses. Western blotting detected photolyase protein in extracts prepared from purified virions and it can be deduced that the poxvirion interior must be fluid enough to permit diffusion of this approximately 50-kDa DNA-binding protein to the sites where it catalyzes photoreactivation. Photolyase promoters are difficult to categorize using bioinformatics methods, as they do not obviously resemble any of the known poxvirus promoter motifs. By fusing the SFV promoter to DNA encoding a luciferase open reading frame, the photolyase promoter was found to exhibit very weak late promoter activity. These data show that the genomes of Leporipoxviruses, similar to that of fowlpox virus, encode catalytically active photolyases. Phylogenetic studies also confirmed the monophyletic origin of poxviruses and suggest an ancient origin for these genes and perhaps poxviruses.

Leporipoxvirus Cu-Zn superoxide dismutase homologs inhibit cellular superoxide dismutase, but are not essential for virus replication or virulence.

Vertebrate poxviruses encode homologs of cellular cupro-zinc superoxide dismutases (Cu-Zn SOD). In this study we have examined the molecular genetic properties of two Cu-Zn SOD homologs encoded by the Shope fibroma virus (SFV) and myxoma virus. These Leporipoxvirus proteins should be catalytically inactive as judged by the point mutations which alter a key catalytic arginine and restructure the predicted Cu-binding domain. This prediction was confirmed using in situ gel assays and recombinant proteins produced both in bacteria and in mammalian cells. Western blot analysis showed that these proteins are produced in abundance late in infection and can, upon exposure to oxidizing conditions, form disulfide cross-linked dimers. They are also virion components and not essential for growth in culture or virulence. Leporipoxvirus Cu-Zn SOD homologs affected two phenotypes. First, deletion of the myxoma M131R gene caused the mutant virus to grow better ( approximately 10-fold) in culture than does the wild-type parent. Second, expression of either native or recombinant Leporipoxvirus proteins is accompanied by a decline in cellular Cu-Zn SOD activity. We concluded that these gene products can somehow modulate the activity of host Cu-Zn SODs, but what advantage is thus gained by the virus remains to be established.

The complete genome sequence of shope (rabbit) fibroma virus.

We have determined the complete DNA sequence of the Leporipoxvirus Shope fibroma virus (SFV). The SFV genome spans 159.8 kb and encodes 165 putative genes of which 13 are duplicated in the 12.4-kb terminal inverted repeats. Although most SFV genes have homologs encoded by other Chordopoxvirinae, the SFV genome lacks a key gene required for the production of extracellular enveloped virus. SFV also encodes only the smaller ribonucleotide reductase subunit and has a limited nucleotide biosynthetic capacity. SFV preserves the Chordopoxvirinae gene order from S012L near the left end of the chromosome through to S142R (homologs of vaccinia F2L and B1R, respectively). The unique right end of SFV appears to be genetically unstable because when the sequence is compared with that of myxoma virus, five myxoma homologs have been deleted (C. Cameron, S. Hota-Mitchell, L. Chen, J. Barrett, J.-X. Cao, C. Macaulay, D. Willer, D. Evans, and G. McFadden, 1999, Virology 264, 298-318). Most other differences between these two Leporipoxviruses are located in the telomeres. Leporipoxviruses encode several genes not found in other poxviruses including four small hydrophobic proteins of unknown function (S023R, S119L, S125R, and S132L), an alpha 2, 3-sialyltransferase (S143R), a protein belonging to the Ig-like protein superfamily (S141R), and a protein resembling the DNA-binding domain of proteins belonging to the HIN-200 protein family S013L). SFV also encodes a type II DNA photolyase (S127L). Melanoplus sanguinipes entomopoxvirus encodes a similar protein, but SFV is the first mammalian virus potentially capable of photoreactivating ultraviolet DNA damage.

The complete DNA sequence of myxoma virus.

Myxomatosis in European rabbits is a severely debilitating disease characterized by profound systemic cellular immunosuppression and a high rate of mortality. The causative agent, myxoma virus, is a member of the poxvirus family and prototype of the Leporipoxvirus genus. As a major step toward defining the genetic strategies by which the virus circumvents host antiviral responses, the genomic DNA sequence of myxoma virus, strain Lausanne, was determined. A total of 171 open reading frames were assigned to cover the 161.8-kb genome, including two copies each of the 12 genes that map within the 11.5-kb terminal inverted repeats. Database searches revealed a central core of approximately 120 kb that encodes more than 100 genes that exhibit close relationships to the conserved genes of members of other poxvirus genera. Open reading frames with predicted signal sequences, localization motifs, or homology to known proteins with immunomodulatory or host-range functions were examined more extensively for predicted features such as hydrophobic regions, nucleic acid binding domains, ankyrin repeats, serpin signatures, lectin domains. and structural cysteine spacings. As a result, several novel, potentially immunomodulatory proteins have been identified, including a family with multiple ankyrin-repeat domains, an OX-2 like member of the neural cell adhesion molecule family, a third myxoma serpin, a putative chemokine receptor fragment, two natural killer receptor-like species, and a variety of species with domains closely related to diverse host immune regulatory proteins. Coupled with the genomic sequencing of the related leporipoxvirus Shope fibroma virus, this work affirms the existence of a conserved complement of poxvirus-specific core genes and expands the growing repertoire of virus genes that confer the unique capacity of each poxvirus family member to counter the immune responses of the infected host.

Regulation of p53 gene expression by a poxviral transcription factor.

Identification of regulators of p53 expression is a crucial step in understanding the diverse functions of p53 and its role in cellular homeostasis and responsiveness to insult. Several viral proteins inactivate p53 as a modulator of cell cycle progression and apoptosis. Here, we report that a unique leporipoxviral transcription factor greatly increases levels of p53 mRNA. C7, an early transcription factor from malignant rabbit fibroma virus (MV), is an important determinant of MV virulence. Its effects on cellular gene expression were studied both during MV infection and in isolation, with C7 DNA cloned into a pKC4 expression plasmid. In both settings, C7 caused increased p53 mRNA levels. The increased p53 mRNA reflected new transcription. C7-induced increased transcription was selective: mRNAs for some cellular genes increased but those for many other genes (e.g., Bc12) were unchanged. Immunoblot and immunohistochemical analysis of pKC7-transfected and MV-infected cells showed that increased transcription led to an increase in p53 protein. EMSA analysis suggested that C7 bound the human p53 promoter between -240 and -614 bp. These studies document the direct effects of a viral transcription factor on cellular gene expression, specifically that it upregulates p53 transcription.

Expression of the myxoma virus tumor necrosis factor receptor homologue and M11L genes is required to prevent virus-induced apoptosis in infected rabbit T lymphocytes.

Myxoma virus is a leporipoxvirus that causes a highly lethal virulent disease known as myxomatosis in the European rabbit. An important aspect of myxoma virus pathogenesis is the ability of the virus to productively infect lymphocytes and spread to secondary sites via lymphatic channels. We investigated the infection of the CD4+ T lymphoma cell line RL-5 with myxoma virus and Shope fibroma virus, a related but benign leporipoxvirus, and observed that myxoma virus, but not Shope fibroma virus, was able to productively infect RL-5 cells. We also discovered that infection of RL-5 cells with Shope fibroma virus or attenuated myxoma virus mutants containing disruptions in either the T2 or the M11L gene resulted in the rapid induction of DNA fragmentation, followed by morphological changes and loss in cell integrity characteristic of cell death by apoptosis. Purified exogenous T2 protein was unable to prevent apoptosis, suggesting that T2 functions intracellularly. Thus, myxoma virus T2, originally described as a secreted homologue of the tumor necrosis factor receptor, and M11L, a novel transmembrane species with no known cellular homologue, function to extend virus host range for replication in rabbit T lymphocytes through the inhibition of apoptosis in infected T lymphocytes.

The effect of transcription on genetic recombination in poxvirus-infected cells.

We have examined the effects of transcription on recombination frequencies in poxvirus-infected cells. A synthetic poxviral promoter was shown to function as a hybrid early/late transcription element when fused to a luciferase reporter gene, and then cloned into genetically-marked recombination substrates. These lambda DNA substrates were transfected into cells infected with Shope fibroma virus (SFV) and the recombinants detected by recovering the transfected DNA, packaging it in vitro into infectious particles, and then assaying the yield of recombinants on Escherichia coli. Controls showed that the poxviral promoter conferred no replicative advantage, or disadvantage, on molecules encoding the promoter. Furthermore, the promoter had no detectable effect on the recombination frequency when recombination was measured in the interval immediately adjacent to the promoter-insertion site. However, the promoter did appear to stimulate recombination at a distance, in a manner that appeared to be dependent on the level of transcription, and the effect was observed regardless of whether or not the promoter was present on one or both of the recombinational substrates. The peak of recombinational enhancement was centered about 500 bp away from the promoter element, where the frequency of recombination was 30-50% higher than that seen when the recombinational substrates lacked the promoter. Possible explanations for these observations are discussed.

Myxoma virus and Shope fibroma virus encode dual-specificity tyrosine/serine phosphatases which are essential for virus viability.

Sequence analysis of the genomes of the Leporipoxviruses myxoma virus and Shope fibroma virus (SFV) led to the discovery of open reading frames homologous to the vaccinia H1L gene encoding a soluble protein phosphatase with dual tyrosine/serine specificity. These viral phosphatase genes were subsequently localized to the myxoma BamHI-I fragment and the SFV BamHI-M fragment, and the resulting encoded proteins were designated I1L and M1L, respectively. The localization and orientation of the myxoma I1L and SFV M1L open reading frames within the well conserved central core of the viral genomes closely mirror that of the Orthopoxviruses vaccinia virus and variola virus. The myxoma I1L and SFV M1L phosphatases each contain the conserved tyrosine phosphatase signature sequence motif, (I/V)HCXAGXXR(S/T)G, including the active site cysteine, found previously to be essential for phosphotyrosine dephosphorylation. The vaccinia H1L phosphatase was originally shown to have the ability to dephosphorylate phosphotyrosyl and phosphoseryl residues in vitro. To assess whether this is a common feature of poxvirus phosphatases, myxoma I1L was expressed as a GST-fusion protein, purified, and shown to dephosphorylate substrates containing tyrosine and serine phosphorylated residues, in a similar fashion to vaccinia H1L. A myxoma I1L variant, in which the active site cysteine 110 was mutated to serine, was expressed in a parallel fashion to the wild-type I1L protein and found to be completely deficient in its ability to dephosphorylate both phosphotyrosine and phosphoserine amino acids. In an attempt to ascertain the biological requirement for the myxoma I1L phosphatase, we constructed a recombinant myxoma virus containing a disrupted I1L open reading frame. This I1L mutant virus was able to successfully propagate in tissue culture only in the presence of a wild-type complementing gene, and pure virus clones containing only the disrupted allele were not viable. Thus, we conclude that the myxoma I1L dual specificity phosphatase is an essential factor for virus viability.

Characterization of the Shope fibroma virus DNA ligase gene.

The Shope fibroma virus (SFV) DNA ligase gene has been cloned and sequenced, and the biochemical requirements of the gene product have been determined in vitro. The SFV ligase gene maps to the BamHI L1/L2 boundary and spans 1.7 kb. The gene is predicted to encode a 559-amino-acid protein of M(r) = 63,139 which shares 45% amino acid identity with Orthopoxvirus ligases. The C-terminal two-thirds of the protein appears to encode the catalytic domain and shares distant homology with many ligases. The N-terminal homology is shared between only Orthopoxviruses and Leporipoxviruses and suggests that DNA ligases may be composite structures consisting of two independently evolved protein domains. Although the the gene encodes features characteristic of both early and late poxviral genes, Northern analysis showed that SFV ligase is expressed as a late gene product. In order to prove the identity of the protein it was expressed as a glutathione S-transferase fusion in Escherichia coli, affinity purified, and shown to be a Mg2+.ATP-dependent ligase in vitro. The recombinant protein can also form a covalent ligase.AMP complex characteristic of ATP-dependent DNA ligases. The SFV ligase gene can be disrupted and is thus not essential for viral growth in culture. This was shown by recombining a PCR product, encoding a P7.5 promoter and E. coli guanine phosphoribosyltransferase gene (gpt) into the open reading frame, and selecting for gpt+ viruses. This work provides insights into the evolution of Orthopoxviruses and Leporipoxviruses and strains suitable for a detailed analysis of the role DNA ligases play in poxviral recombination.

A poxvirus protein with a RING finger motif binds zinc and localizes in virus factories.

Shope fibroma virus (SFV) is a Leporipoxvirus closely related to the highly virulent myxoma virus. The DNA sequence of the BamHI N fragment of the SFV DNA genome was determined, and the single complete open reading frame (N1R) was characterized. The protein encoded by the N1R gene was found to contain a C3HC4 RING finger motif at the C terminus. This C3HC4 motif is the hallmark of a growing family of proteins, many of which are involved in regulation of gene expression, DNA repair, or DNA recombination. Complete homologs of the SFV N1R gene were also detected in variola virus, myxoma virus, and vaccinia virus strain IHD-W. In contrast, the gene is completely absent from vaccinia virus strain Copenhagen, and in vaccinia virus strain WR, the open reading frame is truncated prior to the zinc binding domain because of an 11-bp deletion, thus producing a frameshift and premature stop codon. Recombinant N1R protein from SFV was expressed in Escherichia coli and shown to bind zinc in a specific manner. Using fluorescence microscopy to visualize a peptide epitope tag (derived from ICP27 of herpes simplex virus) fused to the N terminus of the poxvirus proteins, we observed that the N1R protein of SFV and its homologs in myxoma virus and vaccinia virus IHD-W were localized primarily to the virus factories in the cytoplasm of infected cells and, to a lesser degree, the host cell nucleus. The truncated protein of vaccinia virus strain WR failed to localize in this manner but instead was observed throughout the cytoplasm.

Identification of a poxvirus gene encoding a uracil DNA glycosylase.

An open reading frame, BamHI D6R, from the central highly conserved region of the Shope fibroma virus (SFV) genome was sequenced and found to have significant homology to that of uracil DNA glycosylases from a number of organisms. Uracil DNA glycosylase catalyzes the initial step in the repair pathway that removes potentially mutagenic uracil from duplex DNA. The D6R polypeptide was expressed in reticulocyte lysates programmed with RNA transcribed from an expression vector containing the T7 RNA polymerase promoter. A highly specific ethidium bromide fluorescence assay of the in vitro translation product determined that the encoded protein does indeed possess uracil DNA glycosylase activity. Open reading frames from other poxviruses, including vaccinia virus (HindIII D4R) and fowlpox (D4), are highly homologous to D6R of SFV and are predicted to encode uracil DNA glycosylases. Identification of the SFV uracil DNA glycosylase provides evidence that this poxviral protein is involved in the repair of the viral DNA genome. Since this enzyme performs only the initial step required for the removal of uracil from DNA, creating an apyrimidinic site, we suggest that other, possibly virus-encoded, repair activities must be present in the cytoplasm of infected cells to complete the uracil excision repair pathway.

Transforming growth factor alpha, Shope fibroma growth factor, and vaccinia growth factor can replace myxoma growth factor in the induction of myxomatosis in rabbits.

The epidermal growth factor (EGF) homologues encoded by vaccinia virus, myxoma virus, and malignant rabbit fibroma virus have been shown to contribute to the pathogenicity of virus infection upon inoculation of susceptible hosts. However, since the primary structures of these growth factors and the disease profiles induced by different poxvirus genera vary substantially, the degree to which the various EGF homologues perform similar roles in viral pathogenesis remains unclear. In order to determine whether different EGF-like growth factors can perform qualitatively similar functions in the induction of myxomatosis in rabbits, we created recombinant myxoma virus variants in which the native growth factor, myxoma growth factor (MGF), was disrupted and replaced with either vaccinia virus growth factor, Shope fibroma growth factor, or rat transforming growth factor alpha. Unlike the control virus containing an inactivated MGF gene, which caused marked attenuation of the disease syndrome and substantially less proliferation of the epithelial cell layers in the conjunctiva and respiratory tract, the recombinant myxoma virus strains expressing heterologous growth factors produced infections which were both clinically and histopathologically indistinguishable from wild-type myxomatosis. We conclude that these poxviral and cellular EGF-like growth factors, which are diverse with respect to primary structure and origin, have similar biological functions in the context of myxoma virus pathogenesis and are mitogenic for the same target cells.

Nucleotide sequence analysis of a unique near-terminal region of the tumorigenic poxvirus, Shope fibroma virus.

Shope fibroma virus (SFV), a tumorigenic poxvirus, has a DNA genome of approximately 160 kb. Previous DNA sequence analysis of SFV has been mainly limited to the terminal inverted repetitions (about 12 kb at each end of the genome) and immediately adjacent regions. We have sequenced a 4 kb fragment located approximately 20 kb from the right-terminal hairpin. Within this region three complete and two partial open reading frames (ORFs) have been identified. Each of the putative polypeptides has sequence similarity to one or more previously identified poxvirus or cellular proteins, with homology to protein kinases, erythrocyte ankyrin and a vaccinia virus virulence-related protein (ORF N1L). The potential significance of these gene products with regard to the phenotype of SFV is discussed.

Sequence and analysis of the BamHI "D" fragment of Shope fibroma virus: comparison with similar regions of related poxviruses.

Differences observed in the virulence of two related leporipoxviruses are closely tied to a particular region of their genomes. For the virulent poxvirus of this pair, malignant rabbit fibroma virus (MV), this region is the BamHI "C" fragment, which is 10.7 kb. For the avirulent poxvirus, Shope fibroma virus, SFV, this region is the corresponding BamHI "D" fragment, which is 13.1 kb. As part of our attempt to understand the virulence of these two viruses, we sequenced these two DNA fragments. The sequence for the BamHI "C" fragment of MV is reported elsewhere (Strayer et al., 1991). We report here the sequence for SFV's BamHI "D" fragment and resultant open reading frames, and compare both DNA and open reading frame structures to those of MV and other known poxviruses. The BamHI "D" fragment of SFV contains 12 open reading frames of 100 amino acids or more, arranged similarly to orf's in MV and vaccinia. Striking similarities between SFV and MV are seen in certain parts of this restriction fragment, including substantial stretches of DNA in which the two viruses are identical. Clear homologies exist between these leporipox virus genomes and those of other related poxviruses. To understand the pathogenesis of virus infection, one must appreciate the structure of those viral genes that play important roles in infection.

Virus-induced loss of class I MHC antigens from the surface of cells infected with myxoma virus and malignant rabbit fibroma virus.

Shope fibroma virus (SFV) is a leporipoxvirus that causes localized benign fibromas in immunocompetent adult rabbits that spontaneously regress due, in part, to a cell-mediated immune response. Myxoma virus (MYX) and malignant rabbit fibroma virus (MRV) are related leporipoxviruses that induce rapidly lethal generalized infections accompanied by tumors and immunosuppression. Because only these latter two viruses are known to compromise cell-mediated antiviral responses, cell surface levels of class I MHC molecules in SFV-, MRV-, and MYX-infected cells were investigated by fluorescent activated cell sorting analysis using a variety of different anti-HLA mAb. After infection with MYX or MRV there is a rapid decrease in the levels of detectable surface class I epitopes as detected by each antibody and by 24 h postinfection class I MHC Ag levels at the cell surface approach the level of background fluorescence observed with control antibodies. In contrast, only a moderate class I decrease is seen during infection with either SFV or vaccinia virus, an orthopoxvirus that is neither tumorigenic nor immunosuppressive. Surface class I marker loss induced by MYX and MRV is not simply due to nonspecific inhibition of total cellular protein synthesis by the viruses because class I levels decrease much further than the extent measured by estimating surface marker turnover in the presence of the protein synthesis inhibitor cycloheximide. Thus the loss of cellular surface class I molecules greatly exceeds the drop in level caused by complete blockage of host cell gene expression, and must involve removal or masking of preexisting class I epitopes from the cell surface by MRV/MYX. Cell surface levels of the transferrin receptor are unaffected by MYX and MRV infection, suggesting the observed class I decrease is not a nonspecific effect on total cell surface glycoproteins. Analysis of cells infected with MRV/MYX in the presence of cycloheximide or of cytosine arabinoside, an inhibitor of poxviral DNA replication, indicates that the class I marker loss is mediated in part by one or more viral late gene products. A probable explanation is that MRV/MYX late protein(s) interact with the class I MHC complex to either physically sequester these away from the cell surface and inhibit their recycling or else induce a conformational change that precludes recognition by all class I antibodies tested. In either event, we propose that such a major perturbation of the class I MHC complex would likely downregulate the class I-mediated presentation of viral Ag required to initiate cell-mediated immunity to these viruses.

Deletion of the growth factor gene related to EGF and TGF alpha reduces virulence of malignant rabbit fibroma virus.

The role of the epidermal growth factor homologue in malignant rabbit fibroma virus (MRV) pathogenicity was investigated by constructing a viral growth factor deletion mutant (MRV-GF-). Since MRV is a recombinant virus with a myxoma virus background but possesses some terminal sequences derived from Shope fibroma virus, the growth factor gene in MRV is in fact identical to Shope fibroma growth factor (SFGF). Although no significant differences were detected in the in vitro characteristics of MRV and MRV-GF-, a pronounced attenuation was observed after inoculation of the test rabbits with MRV-GF-. Animals infected with wild-type MRV uniformly developed a fatal syndrome involving disseminated tumors accompanied by purulent conjunctivitis and rhinitis. In contrast, although MRV-GF- recipients developed similar initial signs of the MRV disease syndrome, 75% of these animals completely recovered from the viral and secondary bacterial infections and became immune to subsequent MRV challenge. Tumors in MRV-GF- recipients displayed earlier and more prominent inflammatory reactions than their wild-type MRV counterparts and contained fewer proliferating cells. Squamous metaplasia and hyperplasia of target epithelia were less pronounced in MRV-GF- than in MRV infection. We conclude that SFGF is a major virulence factor in MRV infection and is responsible for at least some of the cellular proliferation observed at tumor sites. In addition, the diminished ability of MRV-GF- to cause hyperplasia in nasal and conjunctival epithelia may decrease the extent of gram negative bacterial overgrowth as compared to the parental virus and hence contribute to the dramatic reduction in the lethality of MRV-GF- infection.

Sequence and analysis of a portion of the genomes of Shope fibroma virus and malignant rabbit fibroma virus that is important for viral replication in lymphocytes.

The 10.7-kb BamHI "C" restriction fragment of malignant rabbit fibroma virus (MV) contains genes that are important for its immunosuppressive activity. When this fragment is transferred to a related avirulent leporipoxvirus, Shope fibroma virus (SFV), recombinant viruses show clinical features characteristic of MV: they replicate in lymphocytes and alter immune function in vitro, induce disseminated tumors in recipient rabbits, and are immunosuppressive in vivo. The 10.7-kb BamHI "C" restriction fragment of MV was sequenced in its entirety. Its DNA sequence and the 14 ORF's derived from analyzing this sequence are discussed. Analysis of known open reading frames to which the ORF's from MV's Bam "C" fragment show homology permits us to identify some MV ORF's showing high degrees of similarity to known and postulated proteins produced by vaccinia virus. Functions for some of these vaccinia proteins are known, while functions for others are hypothetical or unknown. Further analysis of genetic determinants of MV's virulence has indicated that two overlapping restriction subfragments of the BamHI "C" fragment can transfer MV's virulent behavior to SFV. The 0.7-kb region in which these two subfragments overlap includes the C-terminus of MV orf C-7 and the N terminus of MV orf C-8. These correspond to the C- and N-termini, respectively, of SFV orf's D-9 and D-10 and to vaccinia orf's D-6 (early transcription factor) and D-7 (subunit of RNA polymerase). We sequenced the region of SFV's BamHI "D" fragment in this area and illustrate here the comparative sequences of this portion of SFV's genome and orf's. On the basis of comparisons between MV, SFV, and vaccinia in this area we discuss the potential significance of these observations.

Enhanced recombination associated with the presence of insertion and deletion mutations in poxvirus-infected cells.

Genetic crosses were performed in cells infected by Shope fibroma virus in order to determine whether poxviral recombination is influenced by the types of mutations participating in a cross. Infected cells were cotransfected with marked bacteriophage lambda DNAs and, after DNA recovery, the substrates were packaged into infectious particles using in vitro packaging extracts. This made it possible to analyze the products of poxviral recombination systems using lambda mutants plated on Escherichia coli. It was observed that, regardless of the kind of substitution, all point mutations recombined in virus-infected cells with frequency dependent only on distance. In contrast, when crosses were performed when one of the mutations was an insertion or a deletion, recombination was stimulated by amounts ranging from 20 to 100%. This phenomenon was not dependent on the size of the nonhomology, was observed across a range of marker separations, and was not due to packaging, plating, or reversion artifacts. The best explanation for this marker effect is that regions of nonhomology act to block the migration of strand-exchange intermediates thereby forcing exchange in the immediate vicinity of a nonhomology. This hypothesis is compatible with the failure to detect loop-heteroduplex intermediates and the specific effects of altered marker configurations in four-factor crosses. It is also compatible with the observation that when two nonhomologies were crossed, they appeared to inhibit recombination in the region located between the two elements. These observations suggest a possible way in which poxviral recombination might be targetted into, or away from, regions of particular interest. The similarities between these observations and data derived from phage and fungal experiments also provide fundamental insights into the mechanism of poxviral recombination.

Heteroduplex DNA formation is associated with replication and recombination in poxvirus-infected cells.

Poxviruses are large DNA viruses that replicate in the cytoplasm of infected cells and recombine at high frequencies. Calcium phosphate precipitates were used to cotransfect Shope fibroma virus-infected cells with different DNA substrates and the recombinant products assayed by genetic and biochemical methods. We have shown previously that bacteriophage lambda DNAs can be used as substrates in these experiments and recombinants assayed on Escherichia coli following DNA recovery and in vitro packaging. Using this assay it was observed that 2-3% of the phage recovered from crosses between point mutants retained heteroduplex at at least one of the mutant sites. The reliability of this genetic analysis was confirmed using DNA substrates that permitted the direct detection of heteroduplex molecules by denaturant gel electrophoresis and Southern blotting. It was further noted that heteroduplex formation coincided with the onset of both replication and recombination suggesting that poxviruses, like certain bacteriophage, make no clear biochemical distinction between these three processes. The fraction of heteroduplex molecules peaked about 12-hr postinfection then declined later in the infection. This decline was probably due to DNA replication rather than mismatch repair because, while high levels of induced DNA polymerase persisted beyond the time of maximal heteroduplex recovery, we were unable to detect any type of mismatch repair activity in cytoplasmic extracts. These results suggest that, although heteroduplex molecules are formed during the progress of poxviral infection, gene conversion through mismatch repair probably does not produce most of the recombinants. The significance of these observations are discussed considering some of the unique properties of poxviral biology.