DNA-binding proteins present in varicella-zoster virus-infected cells

The early UL31 gene of equine herpesvirus 1 encodes a single-stranded DNA-binding protein that has a nuclear localization signal sequence at the C-terminus

The amino acid sequence of the UL31 protein (UL31P) of equine herpesvirus 1 (EHV-1) has homology to that of the ICP8 of herpes simplex virus type 1 (HSV-1). Here we show that the UL31 gene is synergistically trans-activated by the IEP and the UL5P (EICP27). Detection of the UL31 RNA transcript and the UL31P in EHV-1-infected cells at 6h post-infection (hpi) as well as metabolic inhibition assays indicated that UL31 is an early gene. The UL31P preferentially bound to single-stranded DNA over double-stranded DNA in gel shift assays. Subcellular localization of the green fluorescent protein (GFP)-UL31 fusion proteins revealed that the C-terminal 32 amino acid residues of the UL31P are responsible for the nuclear localization. These findings may contribute to defining the role of the UL31P single-stranded DNA-binding protein in EHV-1 DNA replication.

A sequence within the varicella-zoster virus (VZV) OriS is a negative regulator of DNA replication and is bound by a protein complex containing the VZV ORF29 protein

The architecture of the varicella-zoster virus (VZV) origin of DNA replication (OriS) differs significantly from that of the herpes simplex virus (HSV) DNA replication origin. Novel aspects of the VZV OriS include a GA-rich region, three binding sites for the VZV origin-binding protein (OBP) all on the same strand and oriented in the same direction, and a partial OBP binding site of unknown function. We have designated this partial binding site Box D and have investigated the role it plays in DNA replication and flanking gene expression. This has been done with a model system using a replication-competent plasmid containing OriS and a replication- and transcription-competent dual-luciferase reporter plasmid containing both the OriS and the intergenic region between VZV open reading frames (ORFs) 62 and 63. We have found that (i) Box D is a negative regulator of DNA replication independent of flanking gene expression, (ii) the mutation of Box D results in a decrease in flanking gene expression, thus a sequence within the VZV OriS affects transcription, which is in contrast to results reported for HSV-1, (iii) there is a specific Box D complex formed with infected cell extracts in electrophoretic mobility shift assay experiments, (iv) supershift assays show that this complex contains the VZV ORF29 single-strand DNA-binding protein, and (v) the formation of this complex is dependent on the presence of CGC motifs in Box D and its downstream flanking region. These findings show that the VZV ORF29 protein, while required for DNA replication, also plays a novel role in the suppression of that process.

Genome-wide mutagenesis reveals that ORF7 is a novel VZV skin-tropic factor

The Varicella Zoster Virus (VZV) is a ubiquitous human alpha-herpesvirus that is the causative agent of chicken pox and shingles. Although an attenuated VZV vaccine (v-Oka) has been widely used in children in the United States, chicken pox outbreaks are still seen, and the shingles vaccine only reduces the risk of shingles by 50%. Therefore, VZV still remains an important public health concern. Knowledge of VZV replication and pathogenesis remains limited due to its highly cell-associated nature in cultured cells, the difficulty of generating recombinant viruses, and VZV's almost exclusive tropism for human cells and tissues. In order to circumvent these hurdles, we cloned the entire VZV (p-Oka) genome into a bacterial artificial chromosome that included a dual-reporter system (GFP and luciferase reporter genes). We used PCR-based mutagenesis and the homologous recombination system in the E. coli to individually delete each of the genome's 70 unique ORFs. The collection of viral mutants obtained was systematically examined both in MeWo cells and in cultured human fetal skin organ samples. We use our genome-wide deletion library to provide novel functional annotations to 51% of the VZV proteome. We found 44 out of 70 VZV ORFs to be essential for viral replication. Among the 26 non-essential ORF deletion mutants, eight have discernable growth defects in MeWo. Interestingly, four ORFs were found to be required for viral replication in skin organ cultures, but not in MeWo cells, suggesting their potential roles as skin tropism factors. One of the genes (ORF7) has never been described as a skin tropic factor. The global profiling of the VZV genome gives further insights into the replication and pathogenesis of this virus, which can lead to improved prevention and therapy of chicken pox and shingles.

The Varicella Zoster Virus (VZV) is the causative agent of chicken pox and shingles. The long-term efficacy of the current chickenpox vaccine is yet to be determined, and the current shingles vaccine fails to provide protective immunity for a substantial number of individuals. Shingles can also lead to post-herpetic neuralgia (PHN), a debilitating condition associated with an intractable pain that can linger for life. Therefore, VZV remains an important public health concern. We use growth-rate analysis of our genome-wide deletion library to determine the essentiality of all known VZV genes, including novel annotations for 51% of the VZV proteome. We also discovered a novel skin-tropic factor encoded by ORF7. Overall, our identification of genes essential for VZV replication and pathogenesis will serve as the basis for multiple in-depth genetic studies of VZV, which can lead to improved prevention and therapy of chicken pox and shingles. For example, essential genes may be appealing drug targets and genes whose deletion causes a substantial growth defect may be prospective candidates for novel live attenuated vaccines.

The cellular localization pattern of Varicella-Zoster virus ORF29p is influenced by proteasome-mediated degradation

Varicella-zoster virus (VZV) open reading frame 29 (ORF29) encodes a single-stranded DNA binding protein. During lytic infection, ORF29p is localized primarily to infected-cell nuclei, whereas during latency it appears in the cytoplasm of infected neurons. Following reactivation, ORF29p accumulates in the nucleus. In this report, we analyze the cellular localization patterns of ORF29p during VZV infection and during autonomous expression. Our results demonstrate that ORF29p is excluded from the nucleus in a cell-type-specific manner and that its cellular localization pattern may be altered by subsequent expression of VZV ORF61p or herpes simplex virus type 1 ICP0. In these cases, ORF61p and ICP0 induce nuclear accumulation of ORF29p in cell lines where it normally remains cytoplasmic. One cellular system utilized by ICP0 to influence protein abundance is the proteasome degradation pathway. Inhibition of the 26S proteasome, but not heat shock treatment, resulted in accumulation of ORF29p in the nucleus, similar to the effect of ICP0 expression. Immunofluorescence microscopy and pulse-chase experiments reveal that stabilization of ORF29p correlates with its nuclear accumulation and is dependent on a functional nuclear localization signal. ORF29p nuclear translocation in cultured enteric neurons and cells derived from an astrocytoma is reversible, as the protein's distribution and stability revert to the previous states when the proteasomal activity is restored. Thus, stabilization of ORF29p leads to its nuclear accumulation. Although proteasome inhibition induces ORF29p nuclear accumulation, this is not sufficient to reactivate latent VZV or target the immediate-early protein ORF62p to the nucleus in cultured guinea pig enteric neurons.

Dissection of a novel nuclear localization signal in open reading frame 29 of varicella-zoster virus

Open reading frame 29 (ORF29) of varicella-zoster virus (VZV) encodes a 120-kDa single-stranded DNA binding protein (ORF29p) that is not packaged in the virion and is expressed during latency. During lytic infection, ORF29p is localized primarily to infected cell nuclei. In contrast, ORF29p is found exclusively in the cytoplasm in neurons of the dorsal root ganglia obtained at autopsy from seropositive latently infected patients. ORF29p accumulates in the nuclei of neurons in dorsal root ganglia obtained at autopsy from patients with active zoster. The localization of this protein is, therefore, tightly correlated with the proposed VZV lytic/latent switch. In this report, we have investigated the nuclear import mechanism of ORF29p. We identified a novel nuclear targeting domain bounded by amino acids 9 to 154 of ORF29p that functions independent of other VZV-encoded factors. In vitro import assays in digitonin-permeabilized HeLa cells reveal that ORF29p is transported into the nucleus by a Ran-, karyopherin alpha- and beta-dependent mechanism. These data are further supported by the demonstration that a glutathione S-transferase-karyopherin alpha fusion interacts with ORF29p, but not with a protein containing a point mutation in its nuclear localization signal (NLS). Therefore, the region of ORF29p responsible for its nuclear targeting is also involved in the association with karyopherin alpha. As a result of this interaction, this noncanonical NLS appears to hijack the classical cellular nuclear import machinery. Elucidation of the mechanisms governing ORF29p nuclear targeting could shed light on the VZV reactivation process.

Cis and trans elements regulating expression of the varicella zoster virus gI gene

We have identified cis- and trans-acting elements involved in the VZV IE62 protein-activated expression of the varicella zoster virus (VZV) gene which encodes the viral gI glycoprotein. The cis-acting elements include a non-canonical TATA box and a novel 19 base pair sequence located just upstream of the TATA element designated the "activating upstream sequence" or AUS. The AUS is a movable element and its presence results in IE62 activation of a chimeric promoter consisting of the VZV gC TATA box and the gI AUS. We have also determined that the VZV ORF 29 protein modulates the regulatory activity of the IE62 protein at the gI promoter. In combination with the IE62 transactivator, it yields a 10 to 15-fold increase in expression over the levels seen with the IE62 protein alone in T lymphocytes. The upmodulatory activity requires the presence of a 40 base pair sequence, designated the 29RE, which maps between positions -220 and -180 in the gI promoter. In this paper we review these and earlier findings from our laboratories concerning the regulation of the gI promoter.

Physical interaction between two varicella zoster virus gene regulatory proteins, IE4 and IE62

Transfection assays demonstrate that the varicella zoster virus (VZV) immediate-early 62 (IE62) protein is a major transactivator of VZV gene expression, whereas a second immediate-early protein, IE4, can act as a major coactivator of transactivation mediated through IE62. To test whether IE62 and IE4 interact physically, we performed several protein-protein interaction assays. Coimmunoprecipitation analyses using VZV-infected cell lysates as well as purified protein mixtures demonstrate that IE62 and IE4 form stable complexes in solution under stringent salt conditions. Enzyme-linked immunosorbent assay protein-protein interaction assays and maltose-binding protein capture assays demonstrate that IE62 binds IE4 in a concentration- and dose-dependent manner. Far Western blot analyses show that IE4 binds to an undermodified form of IE62, and the use of calf intestinal phosphatase and protein kinases suggests that the interaction with IE4 is dependent on the phosphorylation state of IE62. An IE4 binding domain on IE62 has been mapped using a set of truncated IE62 fusion peptides. Collectively, these results imply a direct and specific physical interaction between IE4 and less-phosphorylated forms of IE62. These data have implications for virion assembly, as well as for the regulation of gene expression in VZV-infected cells.

Mapping of transcriptional regulatory domains of pseudorabies virus immediate-early protein

The 180 kilodalton immediate-early protein (IE180) of pseudorabies virus functions as a strong transactivator of several different promoters and also as a repressor of its own transcription. To map the functional domains of IE180, we prepared various truncated mutants and analyzed their transcriptional regulatory activities using the chloramphenicol acetyl transferase (CAT) assay. Analysis of mutants truncated from the carboxy-terminal end of the 1,460-amino acid polypeptide showed that a polypeptide possessing amino acids 1 to 1,081 retained significant functions of transactivation and autoregulation potential. On the other hand, removing amino acids 1 to 131 resulted in a complete loss of transactivation potential, indicating that the domain responsible for transactivation is located in the amino-terminal end of IE180. Additional amino-terminal truncation up to amino acid 453 did not affect the autoregulation activity, indicating that the region between amino acids 454 and 1081 has autoregulation potential.

Immunization with the immediate-early tegument protein (open reading frame 62) of varicella-zoster virus protects guinea pigs against virus challenge

The IE62 protein, the primary regulatory protein of varicella-zoster virus (VZV) and the major component of the virion tegument, was an effective immunogen in the guinea pig model of VZV infection, whereas the ORF 29 gene product, a nonstructural DNA replication protein, did not elicit protection. All animals immunized with the ORF 29 protein had cell-associated viremia compared with 2 of 11 guinea pigs given the IE62 protein (P = 0.005). VZV was detected in ganglia from 38% of the animals given the ORF 29 protein and 44% of the control animals compared with 9% of the animals immunized with the IE62 protein (P = 0.04). In contrast to the IE62 protein, immunization with the ORF 29 protein did not prime the animals for an enhanced T-cell response upon challenge with infectious virus. The VZV IE62 protein has potential value as a vaccine component.

The varicella-zoster virus immediate-early protein IE62 is a major component of virus particles

Varicella-zoster virus (VZV) open reading frame (ORF) 62 potentially encodes a protein with considerable amino acid homology to the herpes simplex virus (HSV) immediate-early regulatory polypeptide ICP4 (or IE3). To identify and characterize its protein product(s) (IE62), we used a rabbit antiserum prepared against a synthetic peptide corresponding to the C-terminal 13 amino acids of the predicted protein. This antiserum reacted with phosphorylated polypeptides of 175 to 180 kDa that were made in VZV-infected cells and in cells infected with a vaccinia virus recombinant expressing IE62, but not in control-infected cells, confirming its specificity and reactivity to the IE62 protein. The antiserum recognized a 175-kDa polypeptide in purified virions that comigrated with a major structural protein. Comparison of this reactivity with that of an antipeptide antiserum directed against the VZV ORF 10 product (homologous to the HSV major structural protein VP16) indicates similar levels of ORF 62 and ORF 10 polypeptides in VZV virions. In contrast, antipeptide antiserum directed against the VZV ORF 29 product, the homolog of the HSV major DNA-binding protein, failed to recognize any protein in our virion preparations. Treatment of virions with detergents that disrupt the virion envelope did not dissociate IE62 from the nucleocapsid-tegument structure of the virion. Differential sensitivity of VZV virion IE62 to trypsin digestion in the presence or absence of Triton X-100 indicates that IE62 is protected from trypsin degradation by the virus envelope; since it is not a nucleocapsid protein, we conclude that it is part of the tegument. Finally, we show that the virion 175-kDa protein either can autophosphorylate or is a major substrate in vitro for virion-associated protein kinase activity.

The conserved DNA-binding domains encoded by the herpes simplex virus type 1 ICP4, pseudorabies virus IE180, and varicella-zoster virus ORF62 genes recognize similar sites in the corresponding promoters

Herpes simplex virus types 1 and 2 (HSV-1 and HSV-2), pseudorabies virus (PRV), varicella-zoster virus (VZV), and equine herpesvirus 1 (EHV-1) are all classified as Alphaherpesvirinae. Each of these five viruses encodes an essential immediate-early (IE) regulatory protein referred to as HSV-1 ICP4, HSV-2 ICP4, PRV IE180, VZV ORF62 protein, and EHV-1 IE1, respectively. These five proteins share extensive homology with each other in domains referred to as regions 2 and 4. The HSV-1 ICP4 region 2 domain contains residues that are required for the DNA-binding capability of ICP4. In this report, we describe the expression of region 2 domains from the ICP4, IE180, and ORF62 genes as fusion proteins in Escherichia coli. DNA-binding assays revealed that each of these region 2 fusion proteins binds to a sequence that overlaps the transcription start site in the promoter for the gene encoding the corresponding protein. Each of the sites with high affinity for one or more of these fusion proteins contains the sequence 5'-ATCGT-3'. This sequence spans the mRNA cap site in the HSV-2 ICP4 gene promoter and is immediately upstream from the transcription start site in the EHV-1 IE1 gene. These results suggest that formation of a specific complex between an IE protein and its own gene promoter may be a common mechanism used by Alphaherpesvirinae to autoregulate transcription of an essential IE gene.

The glycoprotein products of varicella-zoster virus gene 14 and their defective accumulation in a vaccine strain (Oka)

Many characteristics of the putative protein encoded by varicella-zoster virus (VZV) open reading fram (ORF) 14 indicate that it is a glycoprotein, which has been designated gpV. To identify the protein products of the gene, the coding sequences were placed under the control of the vaccinia virus p7.5 promoter and recombinant vaccinia viruses were constructed. Heterogeneous polypeptides with molecular weights of 95,000 to 105,000 (95K to 105K polypeptides) were expressed in cells infected by a vaccinia virus recombinant (vKIP5) containing ORF 14 from VZV Scott but were not expressed by control vaccinia viruses. These polypeptides were recognized by antibodies present in human sera that contained high levels of anti-VZV antibodies. Conversely, antisera raised in rabbits inoculated with vKIP5 reacted specifically with heterogeneous 95K to 105K polypeptides present in VZV Scott-infected but not uninfected cells; these polypeptides show a patchy plasma membrane fluorescence pattern in VZV Scott-infected cells. These same antisera neutralized VZV strain Scott infectivity in the absence of complement. Endoglycosidase F treatment of isolated gpV polypeptides and tunicamycin treatment of cells infected with the vKIP5 recombinant indicated that the polypeptides were glycosylated. Three sets of data imply that the VZV strain Oka, which has been used to produce a live attenuated virus vaccine, accumulates low levels of gpV polypeptides relative to wild-type strains: (i) blocking of antibodies in human sera with excess VZV Oka-infected cell antigen yielded residual antibodies which were reactive with the 95K to 105K gpV polypeptides expressed in cells infected by VZV strain Scott and by the vKIP5 vaccinia virus recombinant, but not with Oka-infected cell polypeptides; (ii) antisera raised to vKIP5 detected very low levels of reactive polypeptides made in VZV Oka-infected cells and neutralized VZV Oka virus much less efficiently than VZV Scott; and (iii) comparisons of the reactivity of sera from live attenuated virus vaccine vaccinees with sera derived from patients recovering from wild-type infections indicated greatly reduced levels of gpV-specific antibodies in some vaccinees.

Characterization of a major DNA-binding domain in the herpes simplex virus type 1 DNA-binding protein (ICP8)

We have studied the major DNA-binding protein (ICP8) from herpes simplex virus type 1 to identify its DNA-binding site. Since we obtained our protein from a cell line carrying multiple chromosomally located copies of the ICP8 gene, we first analyzed this protein to assess its similarity to the corresponding viral protein. Our protein resembled the viral protein by molecular weight, response to antibody, preference for binding single-stranded DNA, and ability to lower the melting temperature of poly(dA-dT). To define the DNA-binding domain, we subjected the protein to limited trypsin digestion and separated the peptide products on a sodium dodecyl sulfate-polyacrylamide gel. These fragments were then transferred to a nitrocellulose membrane, renatured in situ, and tested for their ability to bind DNA. From this assay, we identified four fragments which both bound DNA and exhibited the expected binding preference for single-stranded DNA. The sequence of the smallest of these fragments was determined and corresponds to a polypeptide spanning residues 300 to 849 in the intact protein. This peptide contains several regions which may be important for DNA binding based on sequence similarities in single-stranded DNA-binding proteins from other herpesviruses and, in one case, on a conserved sequence found in more distant procaryotic and eucaryotic proteins.

Identification of the gene homologous to HSV major DNA binding protein in the BHV-1 genome

By means of Southern blot hybridisation using a cloned herpes simplex virus (HSV) major DNA binding protein (MDBP) gene as probe, the putative MDBP gene of BHV-1 was located within the Hind III G fragment which mapped between 0.352 and 0.381 map units of the BHV-1 genome. Moreover, an antiserum raised to HSV MDBP precipitated a 120kD polypeptide in a radio-immunoprecipitation test.

Identification and characterization of a varicella-zoster virus DNA-binding protein by using antisera directed against a predicted synthetic oligopeptide

We have identified, in varicella-zoster virus (VZV)-infected cells, the product of the gene predicted to code for the VZV analog of the herpes simplex virus major DNA-binding protein. The open reading frame of the VZV gene has the potential to code for a protein with a predicted molecular weight of 132,000 (a 132K protein). To detect the protein, a 12-amino-acid oligopeptide corresponding to the carboxyl terminus of the putative open reading frame was synthesized and used to prepare antisera in rabbits. The resulting antibodies reacted specifically in Western immunoblot analysis and immunoprecipitation with a single 130K polypeptide found in VZV-infected cells. The specific reactivity of the antisera with the 130K polypeptide was inhibited by the addition of synthetic peptide. Immunofluorescence studies with the antisera as probe for the 130K polypeptide suggested that this peptide is located predominantly within the nuclei of infected cells. Analysis of proteins that bind to single-stranded DNA immobilized on cellulose matrices indicated that 30 to 50% of the 130K polypeptide is capable of interacting with single-stranded DNA and that this interaction is overcome with 0.5 M NaCl. Thus, we have prepared a specific polyclonal antiserum that identifies a VZV DNA-binding protein whose properties are similar to those of the herpes simplex virus ICP8 (Vmw130) DNA-binding protein.

Immunological characterization of an early cytomegalovirus single-strand DNA-binding protein with similarities to the HSV major DNA-binding protein

Monospecific polyclonal antisera were prepared against the 129-kDa, early, single-strand DNA-binding protein (DB129) of strain Colburn cytomegalovirus (CMV), and used to study its distribution in infected cells and its relatedness to a proposed human CMV (HCMV) counterpart (DB140). Indirect immunofluorescence of fixed, infected human fibroblasts showed DB129 to be localized within the intranuclear inclusions characteristic of replicating CMV. Treatment of infected cells with 50 to 100 micrograms phosphonoformic acid per milliliter resulted in the overproduction of DB129 and its accumulation within nuclei, both inside the inclusions and in surrounding areas of the nucleoplasm, whereas treatment with 500 micrograms/ml prevented inclusion formation, and DB129 was localized at discrete points throughout the infected-cell nuclei. The sera cross-reacted an estimated 10% with HCMV DB140 in an indirect immunoassay, and their use in immunofluorescence localized DB140 to the nuclear inclusions of HCMV-infected cells. Their immunological cross-reactivity, as well as their similar biochemical properties and intracellular distribution, support the likelihood that DB129 and DB140 are the protein products of homologous genes. The relationship of these proteins to the herpes simplex major DNA-binding protein is discussed.

DNA-binding proteins specified by African swine fever virus

[35S]Methionine-labeled proteins from total or cytoplasmic extracts of Vero cells infected with African swine fever virus were chromatographed on native and denatured DNA-cellulose and DNA-binding proteins were analyzed by SDS-polyacrylamide gel electrophoresis (SDS-PAGE), by DNA binding to Western blots, or by two-dimensional electrophoresis. Thirteen virus-specific DNA-binding proteins were detected by one-dimensional analysis. Major species have molecular mass 44,000 (44K), 38K, 20K, 18K, 14K, 13K, and 12K. The remaining DNA-binding proteins are proteins with molecular mass 130K, 110K, 35K, 33K, 17K, and 14.5K. When viral DNA used in the binding assay the results were very similar but the 13K protein did not bind viral DNA. Seven other minor virus-specific DNA-binding proteins could be detected by two-dimensional analysis. This technique also enabled the assignment of virus-specific proteins. Seven of the virus-specific DNA-binding proteins are structural proteins. Twelve are late proteins, the remaining being early proteins synthesized before viral DNA replication. Most of the virus-specific DNA-binding proteins bind both to double-stranded and to single-stranded DNA. The 110K, 29K, and 18K DNA-binding proteins bind only to single-stranded DNA. Two virus-specific enzymatic activities, DNA polymerase and RNA polymerase, were present in the fractions separated by DNA-cellulose chromatography. The virus-specific single-stranded DNA nuclease did not bind to DNA.

RNA-binding proteins of coronavirus MHV: detection of monomeric and multimeric N protein with an RNA overlay-protein blot assay

RNA-binding proteins of coronavirus MHV-A59 were identified using an RNA overlay-protein blot assay (ROPBA). The major viral RNA-binding protein in virions and infected cells was the phosphorylated nucleocapsid protein N (50K). A new 140K virus structural protein was identified as a minor RNA-binding protein both in virions and in infected cells. The 140K protein was antigenically related to N, and upon reduction, yielded only 50K N. Thus, the 140K protein is probably a trimer of N subunits linked by intermolecular disulfide bonds. Several cellular RNA-binding proteins were also detected. RNA-binding of N was not nucleotide sequence specific. Single-stranded RNA of MHV, VSV, or cellular origin, a DNA probe of the MHV leader sequence, and double-stranded bovine rotavirus RNA could all bind to N. Binding of MHV RNA was optimal between pH 7 and 8, and the RNA could be eluted in 0.1 M NaCl. The ROPBA is a useful method for the initial identification of RNA-binding proteins, such as N and the 140K protein of murine coronavirus.

Transcription mapping of the varicella-zoster virus genome

RNA was isolated from varicella-zoster virus-infected Flow 5000 cells (diploid fibroblasts) at late times after infection. With the use of overlapping DNA probes representing all regions of the varicella-zoster genome, an extensive Northern blot analysis of the RNA was carried out. The analysis revealed at least 58 discrete transcripts ranging in size from approximately 0.8 to 6.5 kilobases. RNAs were found to be homologous to all probes used except for those mapping at approximately map unit 0.3, where no RNA transcripts could be detected. Comparison of the sizes and locations of RNA transcripts mapping in the right-hand ends of the varicella-zoster virus and the herpes simplex virus DNAs shows a number of striking analogies, suggesting their similar genomic organization.