Purification of the late transcription system of vaccinia virus: identification of a novel transcription factor

Poxvirus transcription

Most DNA viruses selfishly exploit the cellular transcription machinery of infected cells. Poxviruses are unique among DNA viruses in that they encode the majority of the enzymes required for RNA synthesis. Poxviruses are large DNA viruses that replicate entirely within the cytoplasmic compartment of the cell, and they encode their own multisubunit RNA polymerase and gene-specific transcription and termination factors. The virus-encoded RNA polymerase has sequence and structural homology to eukaryotic RNA polymerases. Virus-encoded and cellular proteins regulate promoter specificity by recruiting the viral RNA polymerase to one of three different classes of genes. Functional interplay between viral and cellular transcription factors in viral gene regulation represents a new frontier in poxvirus biology. Targeting these transcription systems may serve as an undeveloped and potent antiviral strategy to combat poxvirus infections.

Vaccinia virus G8R protein: a structural ortholog of proliferating cell nuclear antigen (PCNA)

Background

Eukaryotic DNA replication involves the synthesis of both a DNA leading and lagging strand, the latter requiring several additional proteins including flap endonuclease (FEN-1) and proliferating cell nuclear antigen (PCNA) in order to remove RNA primers used in the synthesis of Okazaki fragments. Poxviruses are complex viruses (dsDNA genomes) that infect eukaryotes, but surprisingly little is known about the process of DNA replication. Given our previous results that the vaccinia virus (VACV) G5R protein may be structurally similar to a FEN-1-like protein and a recent finding that poxviruses encode a primase function, we undertook a series of in silico analyses to identify whether VACV also encodes a PCNA-like protein.

Results

An InterProScan of all VACV proteins using the JIPS software package was used to identify any PCNA-like proteins. The VACV G8R protein was identified as the only vaccinia protein that contained a PCNA-like sliding clamp motif. The VACV G8R protein plays a role in poxvirus late transcription and is known to interact with several other poxvirus proteins including itself. The secondary and tertiary structure of the VACV G8R protein was predicted and compared to the secondary and tertiary structure of both human and yeast PCNA proteins, and a high degree of similarity between all three proteins was noted.

Conclusions

The structure of the VACV G8R protein is predicted to closely resemble the eukaryotic PCNA protein; it possesses several other features including a conserved ubiquitylation and SUMOylation site that suggest that, like its counterpart in T4 bacteriophage (gp45), it may function as a sliding clamp ushering transcription factors to RNA polymerase during late transcription.

Protein interactions among the vaccinia virus late transcription factors

The viral proteins A1L, A2L, G8R, and H5R positively modulate vaccinia virus late gene expression. Host-encoded proteins hnRNP A2 and RBM3 may also interact with these viral factors to influence late gene expression. In these studies, a yeast two-hybrid screen and in vitro pulldown and crosslinking experiments were used to investigate protein--protein interactions among these factors. These studies confirmed a previous observation that G8R interacts with itself and A1L. However, self-interactions of A1L and H5R, and interactions between A2L and G8R, A2L and H5R, and H5R and G8R were also observed. In addition, the proteins hnRNP A2 and RBM3 both showed some interaction with A2L. Illustration of these interactions is a step toward understanding the architecture of the late gene transcription complex as it occurs in poxviruses.

Vaccinia virus intermediate stage transcription is complemented by Ras-GTPase-activating protein SH3 domain-binding protein (G3BP) and cytoplasmic activation/proliferation-associated protein (p137) individually or as a heterodimer

Transcription of the DNA genome of vaccinia virus occurs in the cytoplasm and is temporally programmed by early, intermediate, and late stage-specific transcription factors in conjunction with a viral multisubunit RNA polymerase. The RNA polymerase, capping enzyme, and three factors (VITF-1, VITF-2, and VITF-3) are sufficient for in vitro transcription of a DNA template containing an intermediate stage promoter. Vaccinia virus intermediate transcription factor (VITF)-1 and -3 are virus-encoded, whereas VITF-2 was partially purified from extracts of uninfected HeLa cells. Using purified and recombinant viral proteins, we showed that the HeLa cell factor was required for transcription of linear or nicked circular templates but not of super coiled DNA. HeLa cell polypeptides of approximately 110 and 66 kDa copurified with VITF-2 activity through multiple chromatographic steps. The polypeptides were separated by SDS-polyacrylamide gel electrophoresis and identified by mass spectrometry as Ras-GTPase-activating protein SH3 domain-binding protein (G3BP) and p137, recently named cytoplasmic activation/proliferation-associated protein-1. The co-purification of the two polypeptides with transcription-complementing activity was confirmed with specific antibodies, and their association with each other was demonstrated by affinity chromatography of tagged recombinant forms. Furthermore, recombinant G3BP and p137 expressed individually or together in mammalian or bacterial cells complemented the activity of the viral RNA polymerase and transcription factors. The involvement of cellular proteins in transcription of intermediate stage genes may regulate the transition between early and late phases of vaccinia virus replication.

Vaccinia virus transcription

Vaccinia virus replication takes place in the cytoplasm of the host cell. The nearly 200 kbp genome owes part of its complexity to encoding most of the proteins involved in genome and mRNA synthesis. The multisubunit vaccinia virus RNA polymerase requires a separate set of virus-encoded proteins for the transcription of the early, intermediate and late classes of genes. Cell fractionation studies have provided evidence for a role for host cell proteins in the initiation and termination of vaccinia virus intermediate and late gene transcription. Vaccinia virus resembles nuclear DNA viruses in the integration of viral and host proteins for viral mRNA synthesis, yet is markedly less reliant on host proteins than its nuclear counterparts.

Regulation of viral transcription elongation and termination during vaccinia virus infection

Vaccinia virus provides a useful genetic and biochemical tool for studies of the basic mechanisms of eukaryotic transcription. Vaccinia genes are transcribed in three successive gene classes during infection, early, intermediate, and late. Vaccinia transcription is regulated primarily by virus gene products not only during initiation, but also during elongation and termination. The factors and mechanisms regulating early elongation and termination differ from those regulating intermediate and late gene expression. Control of transcription elongation and termination in vaccinia virus bears some similarity to the same process in other prokaryotic and eukaryotic systems, yet features some novel mechanisms as well.

Common origin of four diverse families of large eukaryotic DNA viruses

Comparative analysis of the protein sequences encoded in the genomes of three families of large DNA viruses that replicate, completely or partly, in the cytoplasm of eukaryotic cells (poxviruses, asfarviruses, and iridoviruses) and phycodnaviruses that replicate in the nucleus reveals 9 genes that are shared by all of these viruses and 22 more genes that are present in at least three of the four compared viral families. Although orthologous proteins from different viral families typically show weak sequence similarity, because of which some of them have not been identified previously, at least five of the conserved genes appear to be synapomorphies (shared derived characters) that unite these four viral families, to the exclusion of all other known viruses and cellular life forms. Cladistic analysis with the genes shared by at least two viral families as evolutionary characters supports the monophyly of poxviruses, asfarviruses, iridoviruses, and phycodnaviruses. The results of genome comparison allow a tentative reconstruction of the ancestral viral genome and suggest that the common ancestor of all of these viral families was a nucleocytoplasmic virus with an icosahedral capsid, which encoded complex systems for DNA replication and transcription, a redox protein involved in disulfide bond formation in virion membrane proteins, and probably inhibitors of apoptosis. The conservation of the disulfide-oxidoreductase, a major capsid protein, and two virion membrane proteins indicates that the odd-shaped virions of poxviruses have evolved from the more common icosahedral virion seen in asfarviruses, iridoviruses, and phycodnaviruses.

Vaccinia virus late transcription is activated in vitro by cellular heterogeneous nuclear ribonucleoproteins

Vaccinia virus gene expression is temporally regulated, and three gene classes have been identified: early, intermediate, and late. Several virus-encoded proteins and an activity designated VLTF-X are required for maximum transcription in vitro of a template containing a late promoter. VLTF-X is present in both cytoplasmic and nuclear extracts prepared from uninfected mammalian cells and co-purifies with a late promoter DNA-binding activity. Here, extensive purification of VLTF-X has revealed that heterogeneous nuclear ribonucleoproteins A2/B1 and RBM3 co-purified with in vitro late transcription stimulation. Overexpression and purification of these proteins from Escherichia coli demonstrated that they both complemented for VLTF-X activity in in vitro transcription reactions. These studies identify two host cell factors potentially contributing to poxvirus replication in vivo.

Transcription factor YY1 is a vaccinia virus late promoter activator

Vaccinia virus has a DNA genome, yet replicates in the cytoplasmic compartment of the cell. We previously described the identification of a cellular protein having high affinity for vaccinia virus late promoter DNA. Sequence substitutions in the vaccinia I1L promoter were used to define a 5-nucleotide block at the transcription initiation site as essential for interaction with the protein. Within this sequence is the recognition motif for the nuclear transcription factor YY1. This factor regulates a multitude of cellular promoters, as an activator of transcription, as a repressor, or as an initiator element-binding protein. Antibodies directed against YY1 were used to show that YY1 copurified with the vaccinia late promoter-binding protein and was present in late promoter-protein complexes in gel supershift assays. Bacterially expressed YY1 also bound specifically to late promoter DNA. A dinucleotide replacement within the YY1 recognition motif directly adjacent to the transcription start site severely reduced the affinity of YY1 for the I1L promoter in vitro and impaired I1L promoter-dependent transcription in vivo. The intracellular localization of YY1 was shown by immunofluorescence microscopy to shift from primarily nuclear to the cytoplasm after vaccinia infection. These results indicate that YY1 has a positive role in the regulation of vaccinia virus late gene transcription and suggest that poxviruses have adapted cellular initiator elements as a means of regulating viral gene expression. This is the first identifiable cellular protein implicated in poxvirus transcription.

A vaccinia virus late transcription factor with biochemical and molecular identity to a human cellular protein

A factor designated VLTF-X is required to support vaccinia virus late transcription in vitro. It has been found that a late promoter DNA binding activity cochromatographs and cosediments with VLTF-X activity. Current experiments show that VLTF-X activity is present in a variety of uninfected mammalian cell types and is indistinguishable from that recovered from infected cells based upon several criteria. VLTF-X activity from both sources displays the same purification profile over phosphocellulose and DNA affinity resins and has the same sedimentation coefficient. In addition, the factors purified from both infected and uninfected cells form protein-DNA complexes of identical electrophoretic mobility in the presence of vaccinia virus late promoter-containing DNA. The affinity of these factors for the late promoter probes is identical and late promoter-specific based on competition experiments. Moreover, VLTF-X purified from both sources bound to late promoter-containing DNA in the presence or absence of MgCl2 and ATP and formed complexes resistant to heat inactivation. These experiments offer proof that vaccinia virus factor VLTF-X is a host cell protein that supports transcription of the viral late genes.

A cellular protein binds vaccinia virus late promoters and activates transcription in vitro

Available evidence indicates that the transcription of the late class of vaccinia virus genes requires the participation of several virus-encoded proteins in addition to the viral RNA polymerase. In this report we describe the identification of a protein present in extracts of uninfected HeLa cells that binds avidly to viral late promoter DNA. The protein bound specifically to several different vaccinia virus late promoters but not an early nor an intermediate promoter. DNase I footprinting localized the protein's binding site to nucleotides surrounding the transcriptional start site of the I1L promoter. Optimal promoter binding required sequences in the highly conserved TAAAT motif at the transcriptional start site as well as sequences immediately upstream; however, one variation on the motif's sequence did not affect promoter binding by the protein. Partially purified late promoter binding protein (LPBP) was capable of stimulating the transcription activity of extracts depleted of LPBP on a late promoter-driven template, establishing LPBP as a transcription activator in vitro. These results suggest that a cellular protein is responsible for targeting vaccinia virus late promoters for initiation of transcription.

A vaccinia virus late transcription factor copurifies with a factor that binds to a viral late promoter and is complemented by extracts from uninfected HeLa cells

We have previously described a vaccinia virus late transcription factor, VLTF-X, which we found to be present in cells at early and late times in infection. In this study, transcription complementation assays were used to demonstrate that VLTF-X activity is also present in virion extracts and in the cytoplasm of uninfected HeLa cells. Mobility shift assays performed on various VLTF-X preparations revealed that a late promoter DNA-binding activity cochromatographed and cosedimented with VLTF-X activity. Competition experiments demonstrated that this binding was specific for the late promoter region of the probe and that late transcription was dramatically reduced by an oligonucleotide that blocked factor-DNA complex formation but was only minimally affected by an oligonucleotide that did not inhibit complex formation. These results suggest that a cellular factor may participate in vaccinia virus late transcription. These findings also confirm the requirement for VLTF-X and distinguish it from any of the previously described vaccinia virus late transcription factors, which have all been mapped to the viral genome. Finally, these studies also suggest that the biochemical role for VLTF-X may be in late promoter recognition.

De novo synthesis of the early transcription factor 70-kilodalton subunit is required for morphogenesis of vaccinia virions

Vaccinia virus early transcription factor (VETF) is a heterodimeric protein that is packaged in virus particles for expression of early genes during the next round of infection. To investigate additional roles of VETF, we constructed a conditionally lethal recombinant vaccinia virus in which the D6R gene, encoding the 70-kDa subunit of VETF, is under stringent Escherichia coli lac operator control. When cells were infected with the recombinant virus in the absence of an inducer, synthesis of the 70-kDa protein was undetectable and the yield of infectious virus was severely reduced. Under these nonpermissive conditions, DNA replication and synthesis of viral proteins other than the one encoded by D6R occurred, suggesting that de novo synthesis of VETF is not required for expression of early or late genes during the virus growth cycle. Electron microscopy, however, revealed that immature virus particles and masses of electron-dense material accumulated in the absence of an inducer. We concluded that VETF has a direct role in virion morphogenesis or is required for expression of a novel subset of genes that have such a role.

The vaccinia virus H5R gene encodes late gene transcription factor 4: purification, cloning, and overexpression

The vaccinia virus late stage-specific transcription factor P3 was purified to homogeneity from HeLa cells that were infected in the presence of an inhibitor of viral DNA replication. The purified 36-kDa protein was digested with trypsin, and the peptides were analyzed by mass spectroscopy and amino-terminal sequencing. The purified factor was identified as the product of the vaccinia virus H5R open reading frame by both methods. A recombinant baculovirus was engineered to express the H5R open reading frame. The partially purified recombinant protein could replace the vaccinia virus P3 factor in transcription assays. On the basis of these findings, we assigned the H5R gene product the name viral late gene transcription factor 4 (VLTF-4). Unlike VLTF-1, -2, and -3, which are synthesized exclusively after viral DNA replication, VLTF-4 is synthesized before and after viral DNA synthesis. Indirect immunofluorescence of infected cells with anti-H5R protein antiserum demonstrated that VLTF-4 is diffusely distributed in the cytoplasm when DNA replication is blocked but is localized to discrete viral DNA-containing factories during a productive infection. Its expression pattern and subcellular distribution suggest that the H5R gene product may have multiple roles in the viral life cycle.

Transcription of a vaccinia virus late promoter template: requirement for the product of the A2L intermediate-stage gene

Evidence is presented that a 26-kDa protein encoded by the vaccinia virus A2L open reading frame, originally shown to be one of three intermediate-stage genes that together can transactivate late-stage gene expression in transfection assays (J. G. Keck, C. J. Baldick, and B. Moss, Cell 61:801-809, 1990), is required for in vitro transcription of a template with a late promoter. The critical step in this analysis was the preparation of an extract containing all the required factors except for the A2L protein. This extract was prepared from cells infected with a recombinant vaccinia virus expressing the bacteriophage T7 RNA polymerase in the presence of the DNA synthesis inhibitor cytosine arabinoside and transfected with plasmids containing the two other known transactivator genes, A1L and G8R, under T7 promoter control. Reaction mixtures made with extracts of these cells had background levels of late transcription activity, unless they were supplemented with extracts of cells transfected with the A2L gene. Active transcription mixtures were also made by mixing extracts from three sets of cells, each transfected with a gene (A1L, A2L, or G8R) encoding a separate factor, indicating the absence of any requirement for their coexpression. To minimize the possibility that the A2L protein functions indirectly by activating another viral or cellular protein, this gene was expressed in insect cells by using a baculovirus vector. The partially purified recombinant protein complemented the activity of A2L-deficient cell extracts. Recombinant A1L, A2L, and G8R proteins, all produced in insect cells, together complemented extracts from mammalian cells containing only viral early proteins, concordant with previous in vivo transfection data.

The A2L intermediate gene product is required for in vitro transcription from a vaccinia virus late promoter

Previously, the in vitro late transcription system of vaccinia virus was resolved into four components: the 17- and 30-kDa products of the A1L and G8R intermediate genes, respectively, the viral DNA-dependent RNA polymerase, and an unmapped factor sedimenting at 32 to 38 kDa. Another protein, the 26-kDa product of the A2L open reading frame was predicted to be a late transcription factor on the basis of a transient-expression assay but was not recognized as being necessary for transcriptional activity in vitro. We now report that both the unmapped factor and the 26-kDa protein are required for transcription from a vaccinia virus late promoter in vitro. Since the 26-kDa protein has now been shown to be a trans-activator of late transcription and it is the product of a known gene, we suggest that it be designated VLTF-3.

Vaccinia virus gene A18R encodes an essential DNA helicase

The vaccinia virus A18R protein is a DNA-dependent ATPase that contains the canonical sequence motifs associated with the DEXH group of DNA and RNA helicases. Investigation of A18R protein function during infection indicated it functions in the early and late phases of vaccinia virus transcription. The A18R protein shares sequence similarity with the mammalian DNA helicase ERCC3. The ERCC3 protein has a dual function: it is a component of the transcription factor TFIIH and is an essential participant in the cellular nucleotide excision repair pathway. Here we present evidence that the A18R protein is a DNA helicase that unwinds duplex DNA in a 3'-to-5' direction. The A18R helicase was inactive on RNA-DNA and RNA-RNA hybrids. The A18R unwinding activity was most efficient on DNA substrates with lengths of 20 nucleotides or less, and its unwinding activity was not stimulated by the addition of Escherichia coli single-strand-binding protein (SSB), the bacteriophage T4 gene 32 SSB, or the vaccinia virus I3L protein, a putative SSB. We have used an electrophoretic gel mobility shift assay to show that the A18R protein forms a stable complex with single-stranded DNA, and to a lesser extent RNA, in a reaction that does not require ATP.

The H4 subunit of vaccinia virus RNA polymerase is not required for transcription initiation at a viral late promoter

Chromatography of RNA polymerase purified from vaccinia virions and from vaccinia virus-infected HeLa cells resulted in the separation of populations active for early and late transcription. An RNA polymerase population immunodepleted for the vaccinia virus H4 gene peptide could support late transcription.

Functional organization of variola major and vaccinia virus genomes

Comparison of the genomic organization of variola and vaccinia viruses has been carried out. Molecular factors of virulence of these viruses is the focus of this review. Possible roles of the genes of soluble cytokine receptors, complement control proteins, factors of virus replication, and dissemination in vivo for variola virus pathogenesis are discussed. The existence of "buffer" genes in the vaccinia virus genome is proposed.

The vaccinia virus A18R gene product is a DNA-dependent ATPase

The predicted amino acid sequence of the vaccinia virus gene A18R shows significant homology to the human ERCC3 gene product, which is a member of the DEXH subfamily of the DNA and RNA helicase superfamily II and which plays a role in both RNA polymerase II transcription and nucleotide excision repair of DNA. The vaccinia virus A18R gene product is expressed throughout infection and is encapsidated in virions. Vaccinia virions containing mutant A18R gene product are defective in early viral transcription in vitro, and infection with A18R mutant virus results in aberrant viral transcription late during infection. Thus we hypothesize that the vaccinia virus A18R gene product is a helicase that plays a role in viral transcription and possibly DNA repair. As a first test of this hypothesis, we have affinity purified an amino-terminal polyhistidine-tagged A18R protein and shown that it has DNA-dependent ATPase activity. The A18R ATPase activity is stimulated by both single-stranded and double-stranded DNA and by RNA.DNA hybrids, but not by either single-stranded or double-stranded RNA.

Modification of the cascade model for regulation of vaccinia virus gene expression: purification of a prereplicative, late-stage-specific transcription factor

In vivo and in vitro studies have provided evidence that vaccinia virus late gene transcription factors are intermediate gene products synthesized exclusively after DNA replication. Here, we describe an additional transcription factor (P3 factor) that stimulates late gene transcription between 10- and 40-fold but is made in the absence of viral DNA replication. P3 factor activity was not detected either in uninfected cells or in purified virions. A > 1,500-fold purification of P3 factor was achieved by column chromatography of cytoplasmic extracts prepared from cells infected with vaccinia virus in the presence of a DNA replication inhibitor. P3 factor was stage specific, since it could not substitute for early or intermediate transcription factors. Evidence that late stage-specific transcription factors are made both before and after DNA replication necessitates a modification of the cascade model for vaccinia virus gene regulation.