Reproduction of Poxviruses

Systematic characterization of the local evolutionary space available to human PKR and vaccinia virus K3

The interfaces between host and viral proteins can be dynamic spaces in which genetic variants are continually pursued, giving rise to evolutionary arms races.  One such scenario is found between the mammalian innate immunity protein PKR (protein kinase R) and the poxvirus antagonist K3.  Once activated, PKR phosphorylates the natural substrate eIF2α, which halts protein synthesis within the cell and prevents viral replication. K3 acts as a pseudosubstrate antagonist against PKR by directly antagonizing this halt in protein synthesis, enabling poxviruses to replicate in the cell. Exploring the impact of genetic variants in both PKR and K3 is necessary not only to highlight residues of evolutionary constraint and opportunity but also to elucidate the mechanism by which human PKR is able to subvert a rapidly evolving viral antagonist.  To systematically explore this dynamic interface, we have generated a combinatorial library of PKR and K3 missense variants to be co-expressed and characterized in a high-throughput yeast selection assay. This assay allows us to characterize hundreds of thousands of unique PKR-K3 genetic combinations in a single pooled experiment. Our results highlight specific missense variants available to PKR that subvert the K3 antagonist. We find that improved PKR variants are readily available at sites under positive selection, with limited opportunity at sites interfacing with K3 and eIF2α. Additionally, we find many variants that improve and disable K3 antagonism, suggesting a pliable interface. We reason that this approach can be leveraged to explore the evolutionary plasticity of many other host-virus interfaces.

Synthesis of early vaccinia-virus-specific enzymes under conditions of immediate early gene expression

Cycloheximide reversal experiments in chick embryo fibroblasts and mouse L-929 cells indicate that the poxvirus-induced enzymes DNA polymerase and 'alkaline' DNase are immediate early gene products of the virus. In contrast to the vaccinia-WR-coded enzyme under conditions of immediate early gene expression the cowpox-virus-induced DNA polymerase is made only in very small amounts. The studies are consistent with the notion that all poxvirus-specific early proteins may be immediate early viral gene products.

Biochemical and electron microscopic studies of the replication and composition of milker's node virus

Replication of milker's node virus (MNV) DNA begins 4 to 8 h postinfection, continues to 30 to 36 h postinfection in the cytoplasm of infected, primary bovine embryonic kidney cells, and is accompanied by an inhibition of host nuclear DNA synthesis. Between 20 and 24 h postinfection, newly replicated genomes are incorporated into particles which cosediment with purified MNV. These biochemical measurements could be correlated with the development of MN virions as revealed by electron microscopic analysis of thin sections prepared from infected cells. Analysis of the DNA in purified MNV showed that the virions contained a double-stranded DNA molecule with a molecular weight of 85 x 10(6) to 87 x 10(6) and a guanine-plus-cytosine content of about 63%. After denaturation and sedimentation analysis of MNV DNA in alkaline sucrose gradients, three major DNA species were resolved. These species appeared to represent intact, terminally cross-linked genomes (approximately 75 to 80S); genomes bearing one nick (or with one cross-link removed) (60 to 65S); and complementary, denatured DNA strands released from cross-linked genomes bearing two nicks (or with both cross-links removed) (52 to 55S). Forty [35S]methionine-labeled polypeptides, ranging from approximately 200,000 daltons to 10,000 to 15,000 daltons, were detected by radioautography after polyacrylamide gel electrophoresis of the proteins present in detergent-solubilized MNV preparations. Treatment of MN virions with Nonidet P-40, beta-mercaptoethanol, and sonication released 10 polypeptides, which were apparently located on the surface of virions. Further fractionation of these released polypeptides, followed by electron microscopy and polyacrylamide gel electrophoresis, indicated that a 42,000- to 45,000-dalton polypeptide is a major component of the threadlike tubule structure present on the surface of MN virions.

Heat inactivation of vaccinia virus particle-associated functions: properties of heated particles in vivo and in vitro

The heat inactivation characteristics of several vaccinia virus particle-associated functions known to be involved in the transcription of the genome were examined. All functions were more resistant to heat than infectivity. Noninfectious particles were generated which exhibited significant levels of activity of all enzymes examined, and their properties were investigaed both in vitro and in vivo. RNA was synthesized in vitro by such particles, although transport of the RNA into the surrounding medium was defective. This RNA was larger than that made in normal particles but it was polyadenylated and functioned in vitro as a message coding for normal early proteins. The sequences transcribed were similar to those transcribed in normal particles, and we suggest that the production of abnormally large RNA is due to a defect in transcriptional termination. We could not detect any virus-specific protein or RNA synthesis in cells exposed to these inactivated particles and conclude that the loss of infectivity caused by heating is due to a general decline in the activities of a number of particle functions.

Sequence complexity and relative abundance of vaccinia virus mRNA's synthesized in vivo and in vitro

The sequence complexity and relative abundance of vaccinia virus mRNA's, synthesized in vivo and in vitro, have been measured by DNA-RNA hybridization. Up to 42% of [3H]thymidine-labeled virus DNA can be protected from digestion with nuclease S1, a single-strand specific nuclease, after annealing to excess polyadenylylated mRNA obtained at 7 h after infection. In contrast, only 26% of vaccinia virus DNA is protected when hybridized to polyadenylylated RNA obtained at 2 h after infection in the presence of an inhibitor of DNA synthesis. That the 94 kilobases transcribed early are a subset of the 152 kilobases present late was suggested by hybridization of DNA with a mixture of early and late RNAs. Some control of transcription is lost when virus purified by procedures that include sonic treatment is used for infection since under these conditions similar proportions of DNA are protected by either excess early or late RNA. Excess RNA, synthesized in vitro by enzymes within purified vaccinia virus particles, hybridized to approximately the same fraction of the DNA as did RNA present at late times in vivo. A second type of transcriptional control was demonstrated by kinetic analysis of the hybridization of polyadenylylated RNA to labeled DNA. With virion DNA used as the probe, a single abundance class for early RNA, two classes differing 11-fold in abundance for late RNA, and two classes differing 43-fold in abundance for in vitro RNA were found. To be able to detect high-abundance RNAs of very low sequence complexity, labeled complementary DNA probes to early, late, and in vitro polyadenylylated RNA were used. Evidence that, at late times, RNAs totaling 9 kilobases of sequence complexity are present 40 to 500 times more frequently than the bulk of the virus-specific RNA was obtained. In contrast, the highest abundance class of RNA present at 2 h after infection corresponded to 7 kilobases present in only a 13-fold molar excess over the majority of virus-specific sequences. RNA synthesized in vitro was found to contain a small amount of sequence information, approximately 2 kilobases, which occurred 150 times more frequently than the majority of viral sequences. Studies using hybridization of viral DNA to labeled complementary DNA probes also suggested that 52 to 59% of the polyadenylylated RNA present at 2 h after infection and 82 to 92% of that at 7 h are virus specific.

Evidence for an "early early" vaccinia virus-induced protein which causes a density change of infected L-M cells

The density decrease of vaccinia virus-infected L-M cells observed in a Ficoll density gradient by 2 h postinfection was found to be dependent on RNA synthesis and protein synthesis but independent of DNA synthesis. Using low multiplicities of infection, the required RNA and protein species appeared to be synthesized before parental viral DNA became sensitive to DNase, i.e., while the bulk of input virus was still at the core stage of uncoating. To date only thymidine kinase and a vaccinia virus-specific cell surface antigen (as well as the putative uncoating protein) have been shown to be "early early" proteins, i.e., synthesized while parental viral DNA is still enclosed within the core. Both heat- and UV-inactivated virus failed to cause the cell density decrease. The need for a functioning viral genome implies that the required early early RNA and protein species are virus specific and not cell specific. Thus the protein leading to the density decrease of L-M cells, induced very early after infection with vaccinia virus, represents one of the first bits of viral genetic information expressed after infection. Since antibody-neutralized virus is still capable of causing the phenomenon of cell density decrease, the basis of neutralization of vaccinia virus by specific antibody must be other than by inhibiting early early transcription and/or translation.