Detailed analysis of the mRNAs mapping in the short unique region of herpes simplex virus type 1

Roles of the Different Isoforms of the Pseudorabies Virus Protein Kinase pUS3 in Nuclear Egress

Protein kinases homologous to the US3 gene product (pUS3) of herpes simplex virus (HSV) are conserved throughout the alphaherpesviruses but are absent from betaherpesviruses and gammaherpesviruses. pUS3 homologs are multifunctional and are involved in many processes, including modification of the cytoskeleton, inhibition of apoptosis, and immune evasion. pUS3 also plays a role in efficient nuclear egress of alphaherpesvirus nucleocapsids. In the absence of pUS3, primary enveloped virions accumulate in the perinuclear space (PNS) in large invaginations of the inner nuclear membrane (INM), pointing to a modulatory function for pUS3 during deenvelopment. The HSV and pseudorabies virus (PrV) US3 genes are transcribed into two mRNAs encoding two pUS3 isoforms, which have different aminoterminal sequences and abundances. To test whether the two isoforms in PrV serve different functions, we constructed mutant viruses expressing exclusively either the larger minor or the smaller major isoform, a mutant virus with decreased expression of the smaller isoform, or a mutant with impaired kinase function. Respective virus mutants were investigated in several cell lines. Our results show that absence of the larger pUS3 isoform has no detectable effect on viral replication in cell culture, while full expression of the smaller isoform and intact kinase activity is required for efficient nuclear egress. Absence of pUS3 resulted in only minor titer reduction in most cell lines tested but disclosed a more severe defect in Madin-Darby bovine kidney cells. However, accumulations of primary virions in the PNS do not account for the observed titer reduction in PrV.IMPORTANCE A plethora of substrates and functions have been assigned to the alphaherpesviral pUS3 kinase, including a role in nuclear egress. In PrV, two different pUS3 isoforms are expressed, which differ in size, abundance, and intracellular localization. Their respective role in replication is unknown, however. Here, we show that efficient nuclear egress of PrV requires the smaller isoform and intact kinase activity, whereas absence of the larger isoform has no significant effect on viral replication. Thus, there is a clear distinction in function between the two US3 gene products of PrV.

Direct RNA sequencing on nanopore arrays redefines the transcriptional complexity of a viral pathogen

Characterizing complex viral transcriptomes by conventional RNA sequencing approaches is complicated by high gene density, overlapping reading frames, and complex splicing patterns. Direct RNA sequencing (direct RNA-seq) using nanopore arrays offers an exciting alternative whereby individual polyadenylated RNAs are sequenced directly, without the recoding and amplification biases inherent to other sequencing methodologies. Here we use direct RNA-seq to profile the herpes simplex virus type 1 (HSV-1) transcriptome during productive infection of primary cells. We show how direct RNA-seq data can be used to define transcription initiation and RNA cleavage sites associated with all polyadenylated viral RNAs and demonstrate that low level read-through transcription produces a novel class of chimeric HSV-1 transcripts, including a functional mRNA encoding a fusion of the viral E3 ubiquitin ligase ICP0 and viral membrane glycoprotein L. Thus, direct RNA-seq offers a powerful method to characterize the changing transcriptional landscape of viruses with complex genomes.

Construction and manipulation of a full-length infectious bacterial artificial chromosome clone of equine herpesvirus type 3 (EHV-3)

Equine herpesvirus type 3 (EHV-3) is the causal agent of equine coital exanthema, a disease characterized by pox-like lesions on the penis of stallions and the vulva of mares. Although the complete genomic sequence of EHV-3 has been recently made available, its genomic content remains poorly characterized and the molecular mechanisms of disease development not yet elucidated. In an attempt to facilitate genetic manipulation of EHV-3, we describe here the construction of a full-length infectious bacterial artificial chromosome (BAC) clone of EHV-3. Mini-F vector sequences were inserted into the intergenic region between ORF19 and ORF20 (UL41 and UL40, respectively) of EHV-3 strain C175 by homologous recombination in equine dermal cells (NBL-6). DNA of the resulting recombinant virus was electroporated into E. coli and a full-length EHV-3 BAC clone was recovered. Virus reconstituted after transfection of the EHV-3 BAC into NBL-6 cells showed growth properties in vitro that were indistinguishable from those of the parental virus. To assess the feasibility of mutagenesis of the cloned EHV-3 genome, recombinant viruses targeting the glycoprotein E (gE) gene were generated using Red recombination in E. coli and in vitro growth properties of the recombinant viruses were evaluated. We first repaired the gE (ORF74) coding region, since the parental virus used for BAC cloning specifies a truncated version of the gene, and then created gE-tagged and gE-null versions of the virus. Our results demonstrated that: (i) EHV-3 can be efficiently cloned as a BAC allowing easy manipulation of its genome; (ii) gE is dispensable for EHV-3 growth in vitro and is expressed as a product of approximately 110-kDa in infected cells; (iii) viruses having a deletion compromising gE expression or with a truncation of the cytoplasmic and transmembrane domains are significantly compromised with regard cell-to-cell spread. The cloning of EHV-3 as a BAC simplifies future studies to identify the role of its coding genes in viral pathogenesis and host immune responses.

Identification of a physiological phosphorylation site of the herpes simplex virus 1-encoded protein kinase Us3 which regulates its optimal catalytic activity in vitro and influences its function in infected cells

Us3 is a serine/threonine protein kinase encoded by herpes simplex virus 1 (HSV-1). Here, we report the identification of a physiological Us3 phosphorylation site on serine at position 147 (Ser-147) which regulates its protein kinase activity in vitro. Moreover, mutation of this site influences Us3 function, including correct localization of the enzyme and induction of the usual morphological changes in HSV-1-infected cells. These conclusions are based on the following observations: (i) in in vitro kinase assays, a domain of Us3 containing Ser-147 was specifically phosphorylated by Us3 and protein kinase A, while a mutant domain in which Ser-147 was replaced with alanine was not; (ii) in vitro, alanine replacement of Ser-147 (S147A) in Us3 resulted in significant impairment of the kinase activity of the purified molecule expressed in a baculovirus system; (iii) phosphorylation of Ser-147 in Us3 tagged with the monomeric fluorescent protein (FP) VenusA206K (VenusA206K-Us3) from Vero cells infected with a recombinant HSV-1 encoding VenusA206K-Us3 was specifically detected using an antibody that recognizes phosphorylated serine or threonine residues with arginine at the -3 and -2 positions; and (iv) the S147A mutation influenced some but not all Us3 functions, including the ability of the protein to localize itself properly and to induce wild-type cytopathic effects in infected cells. Our results suggest that some of the regulatory activities of Us3 in infected cells are controlled by phosphorylation at Ser-147.

An HSV-1 gD mutant virus as an entry-impaired live virus vaccine

HSV-1 glycoprotein D (gD) interacts with HVEM and nectin-1 cell receptors to initiate virus entry. We prepared an HSV-1 strain with mutations in the gD gene at amino acid residues 3 and 38 by changing alanine to cysteine and tyrosine to cysteine, respectively (A3C/Y38C). These mutations were constructed with the intent of evaluating infection in vivo when virus enters by HVEM but not nectin-1 receptors and were based on prior reports demonstrating that purified gDA3C/Y38C protein binds to HVEM but not to nectin-1. While preparing a high-titered purified virus pool, the cysteine mutation at position 38 reverted to tyrosine, which occurred on two separate occasions. The resultant HSV-1 strain, KOS-gDA3C, had a single amino acid mutation at residue 3 and exhibited reduced entry into both HVEM and nectin-1 expressing cells. When tested in the murine flank model, the mutant virus was markedly attenuated for virulence and caused only mild disease, while the parental and rescued viruses produced much more severe disease. Thirty days after KOS-gDA3C infection, mice were challenged with a lethal dose of HSV-1 and were highly resistant to disease. The KOS-gDA3C mutation was stable during 30 passages in vitro and was present in each of 3 isolates obtained from infected mice. Therefore, this gD mutant virus impaired in entry may represent a novel candidate for an attenuated live HSV-1 vaccine.

An oncolytic mutant of herpes simplex virus type-1 in which replication is governed by a promoter/enhancer of human papillomavirus type-16

Although herpes simplex virus type-1 (HSV-1) can be used as an oncolytic virus it has the undesirable side effect of neurotoxicity. To create a virus with improved specificity for oral cancer we used a fragment of human papillomavirus type-16, which is frequently found in oral and cervical cancers, but not elsewhere. The upstream regulatory region, URR16, was shown to have a high level of transcriptional activity in three of four oral cancer cell lines but low activity in three cell lines derived from brain cancers. URR16 was therefore placed in HSV-1, replacing the promoter of the essential gene ICP4, and the resulting virus was named HSPV-1. When cells were infected with HSPV-1, ICP4 was expressed at levels that were not associated with the level of activity of URR16. The virus replicated in each type of cell to a final titer that showed a correlation with the level of expression of ICP4, but with no correlation to either the tumor of origin or the presence of HPV sequences in the cells. To find if some function of HSV-1 was affecting the activity of URR16, oral cancer cells were transfected with a URR-reporter construct and were then infected with virus. This induced transcription, which was attributed to immediate-early viral genes other than ICP4. A promoter/enhancer from a papillomavirus therefore has the potential to regulate the functions of an oncolytic strain of HSV-1, and is affected by functions of both the host cell and of HSV-1 itself.

Mapping of key functions of the herpes simplex virus 1 U(S)3 protein kinase: the U(S)3 protein can form functional heteromultimeric structures derived from overlapping truncated polypeptides

Earlier studies have shown that the herpes simplex virus (HSV) U(S)3 encodes two transcriptional units directing the synthesis of the U(S)3 (residues 1 to 481) and U(S)3.5 (residues 77 to 481) protein kinases. Both kinases phosphorylate histone deacetylase 1 (HDAC1) and HDAC2 and enable the expression of genes cotransduced into U2OS cells by recombinant baculoviruses, an activity designated the "helper function." The two kinases differ with respect to antiapoptotic activity. In the studies reported here, we made a series of FLAG-tagged amino- and carboxyl-terminal truncations of U(S)3 and these were tested for antiapoptotic activity, phosphorylation of HDAC1, and the helper function. We report the following. (i) HDAC1 phosphorylation and the helper function were expressed in cells transduced by the truncation encoding residues 182 to 481 but not in cells transduced by the truncation encoding residues 189 to 481 or the amino-terminal polypeptides encompassing the first 188 amino acids. (ii) The self-posttranslational modification requires residues 164 to 481. (iii) The antiapoptotic activity requires both the amino-terminal and the carboxyl-terminal domains, of which the truncated protein containing residues 1 to 163 and that containing residues 164 to 481, respectively, were the smallest fragments tested to be effective. The two domains need not be on the same molecule, but they must overlap. The smallest overlapping pair tested was the fragment containing residues 1 to 181 and that containing residues 164 to 481. Consistent with the hypothesis that the effective overlapping truncations form a heteromultimeric structure, antibody to FLAG coprecipitated untagged U(S)3 from lysates of cells cotransduced with FLAG-tagged, truncated U(S)3 constructs. Although U(S)3 has been reported to be a monomeric enzyme, the results indicate that it can form enzymatically active multimeric structures.

The pseudorabies virus serine/threonine kinase Us3 contains mitochondrial, nuclear and membrane localization signals

The serine/threonine kinase encoded by the Us3 gene is conserved amongst all known alphaherpesviruses. Us3 has been reported to function in a variety of aspects of the virus lifecycle including protection of cells from virus-induced apoptosis, de-envelopment of enveloped virus particles from the perinuclear space and cell-to-cell spread of virus infection. In this report, we examined the sub-cellular localization of the pseudorabies virus (PRV) Us3 homolog. The PRV Us3 gene encodes two proteins termed Us3a and Us3b. Us3a differs from Us3b in that it contains 54 additional N-terminal amino acids. In transfected cells, Us3a localized predominantly to the plasma membrane whereas the Us3b protein localized predominantly to the nucleus. To explore the differences in the localization of the Us3a and Us3b proteins, we fused the amino-terminal 54 amino acids of Us3a to the amino-terminus of the enhanced green fluorescent protein (EGFP). Surprisingly, this fusion protein localized exclusively to mitochondria in transfected cells. Analysis of mutated Us3-EGFP fusion proteins in transfected cells revealed that the carboxy-terminal 101 amino acids of Us3a and Us3b comprises a membrane/vesicular localization domain, and that the N-terminal 102 amino acids of Us3b comprises a nuclear localization domain. We provide a model to rationalize the complex localization of Us3a and Us3b in transfected cells and hypothesize that the mitochondrial, nuclear and membrane localization motifs function in the reported anti-apoptotic, egress and cell-to-cell spread functions of Us3.

Phylogenetic analysis of varicella-zoster virus: evidence of intercontinental spread of genotypes and recombination

A heteroduplex mobility assay was used to identify variants of varicella-zoster virus circulating in the United Kingdom and elsewhere. Within the United Kingdom, 58 segregating sites were found out of the 23,266 examined (0.25%), and nucleotide diversity was estimated to be 0.00063. These are an order of magnitude smaller than comparable estimates from herpes simplex virus type 1. Sixteen substitutions were nonsynonymous, the majority of which were clustered within surface-expressed proteins. Extensive genetic correlation between widely spaced sites indicated that recombination has been rare. Phylogenetic analysis of varicella-zoster viruses from four continents distinguished at least three major genetic clades. Most geographical regions contained only one of these three strains, apart from the United Kingdom and Brazil, where two or more strains were found. There was minimal genetic differentiation (one or fewer substitutions in 1,895 bases surveyed) between the samples collected from Africa (Guinea Bissau, Zambia) and the Indian subcontinent (Bangladesh, South India), suggesting recent rapid spread and/or low mutation rates. The geographic pattern of strain distribution would favor a major influence of the former. The genetic uniformity of most virus populations makes recombination difficult to detect. However, at least one probable recombinant between two of the major strains was found among the samples originating from Brazil, where mixtures of genotypes co-occur.

Insertions in the gG gene of pseudorabies virus reduce expression of the upstream Us3 protein and inhibit cell-to-cell spread of virus infection

The alphaherpesvirus Us4 gene encodes glycoprotein G (gG), which is conserved in most viruses of the alphaherpesvirus subfamily. In the swine pathogen pseudorabies virus (PRV), mutant viruses with internal deletions and insertions in the gG gene have shown no discernible phenotypes. We report that insertions in the gG locus of the attenuated PRV strain Bartha show reduced virulence in vivo and are defective in their ability to spread from cell to cell in a cell-type-specific manner. Similar insertions in the gG locus of the wild-type PRV strain Becker had no effect on the ability of virus infection to spread between cells. Insertions in the gG locus of the virulent NIA-3 strain gave results similar to those found with the Bartha strain. To examine the role of gG in cell-to-cell spread, a nonsense mutation in the gG signal sequence was constructed and crossed into the Bartha strain. This mutant, PRV157, failed to express gG yet had cell-to-cell spread properties indistinguishable from those of the parental Bartha strain. These data indicated that, while insertions in the gG locus result in decreased cell-to-cell spread, the phenotype was not due to loss of gG expression as first predicted. Analysis of gene expression upstream and downstream of gG revealed that expression of the upstream Us3 protein is reduced by insertion of lacZ or egfp at the gG locus. By contrast, expression of the gene immediately downstream of gG, Us6, which encodes glycoprotein gD, was not affected by insertions in gG. These data indicate that DNA insertions in gG have polar effects and suggest that the serine/threonine kinase encoded by the Us3 gene, and not gG, functions in the spread of viral infection between cells.

Genomic organization of the canine herpesvirus US region

Canine herpesvirus (CHV) is an alpha-herpesvirus of limited pathogenicity in healthy adult dogs and infectivity of the virus appears to be largely limited to cells of canine origin. CHV's low virulence and species specificity make it an attractive candidate for a recombinant vaccine vector to protect dogs against a variety of pathogens. As part of the analysis of the CHV genome, the authors determined the complete nucleotide sequence of the CHV US region as well as portions of the flanking inverted repeats. Seven full open reading frames (ORFs) encoding proteins larger than 100 amino acids were identified within, or partially within the CHV US: cUS2, cUS3, cUS4, cUS6, cUS7, cUS8 and cUS9; which are homologs of the herpes simplex virus type-1 US2; protein kinase; gG, gD, gI, gE; and US9 genes, respectively. An eighth ORF was identified in the inverted repeat region, cIR6, a homolog of the equine herpesvirus type-1 IR6 gene. The authors identified and mapped most of the major transcripts for the predicted CHV US ORFs by Northern analysis.

Nucleotide sequences of glycoprotein I and E genes of equine herpesvirus type 4

The nucleotide sequences of the glycoprotein I (gI) and E (gE) genes of equine herpesvirus type 4 (EHV-4) strain TH20 were determined. The predicted region encoding the EHV-4 gI gene is 1,263 nucleotides, corresponding to a polypeptide of 420 amino acids in length. The predicted region encoding the EHV-4 gE gene is 1,647 nucleotides, corresponding to a polypeptide of 548 amino acids in length. The EHV-4 gI and gE genes show 74% and 85% identity at the amino acid level with those of equine herpesvirus type 1 (EHV-1), respectively. Furthermore, we have found an open reading frame homologous to the EHV-1 gene 75, which overlaps in part with the 3' end of EHV-4 gE gene. These sequence data will be useful for development of a modified live vaccine against equine herpesvirus type 1 and 4 infections.

Identification of a potential Marek's disease virus serotype 2 glycoprotein D gene with homology to herpes simplex virus glycoprotein D

The gene of Marek's disease virus (MDV) serotype 2 (MDV2) homologous to glycoprotein D (gD) of herpes simplex virus (HSV) was identified and characterized by its nucleotide and predicted amino acid sequences. The MDV2 gD homologous gene contains an open reading frame capable of specifying a polypeptide of 385 amino acids, which include N- and C-terminal hydrophobic domains consistent with signal and anchor regions, respectively, and two potential N-linked glycosylation sites, one of which was located in a highly conserved region when compared to MDV serotype 1 (MDV1) and herpesvirus of turkeys (HVT). By northern blot analysis using a MDV2 gD-specific DNA probe, two highly abundant polycistronic 6.0 and 4.2 kb transcripts were detected in MDV2-infected cells. The genes encoding MDV2 protein kinase (PK), gD, and glycoprotein I (gI) homologues are transcribed to form 3' coterminal mRNAs of 6.0 kb (encoding PK, gD and gI) and 4.2 kb (encoding gD and gI), respectively. By using rapid amplification cDNA end (RACE) method, several RNA start sites, to be thought those of the 4.2 kb mRNA, were detected in the upstream of MDV2 gD homologue.

Transcriptional analyses of the unique short segment of EHV-1 strain Kentucky A

The unique short (Us) segment of the genome of equine herpesvirus type 1 (EHV-1) strain KyA is comprised of six open reading frames (ORFs) that encode: a) a homolog of the Us2 protein of herpes simplex virus type 1 (HSV-1); b) a serine threonine protein kinase that is a homolog of the HSV-1 Us3 protein; c) a homolog of pseudorabies virus glycoprotein gX and HSV-2 gG; d) a novel glycoprotein, EUS4, not encoded by other herpesviruses sequenced to date; e) a homolog of HSV-1 gD; and f) a homolog of HSV-1 Us9. The KyA strain is a deletion mutant that lacks Us sequences encoding gI, gE, and a potential 10 kD polypeptide, and thus may be useful as a parent virus for the generation of live virus vaccines. To complete the elucidation of the transcriptional program of the Us segment, Northern blot hybridization and S1 nuclease analyses were performed on poly(A)(+)-selected RNA isolated from infected cells maintained under early (phosphonoacetic acid-block) and late conditions. The findings revealed that the gene (EUS2 ORF) encoding the protein kinase is expressed as an early 2.9 kb transcript that overlaps and is 3' coterminal with a 1.6 kb early transcript that encodes the gG/gX homolog (EUS3 ORF). Two transcripts of 1.6 kb and 5.8 kb are 5' coterminal and may both encode the novel glycoprotein gene EUS4. The 1.6 kb transcript terminates at a poly(A) signal site downstream of the EUS4 ORF, and the 5.8 kb transcript terminates within the inverted repeat (IR) segment. Overall, the transcriptional program of the EHV-1 KyA Us segment is complex and exhibits similarities to that of HSV-1 Us segment: a) transcripts arise from both DNA strands; b) some transcripts, including those mapping at the termini of the Us segment, extend into the IR segments and are 3' coterminal with the 1.2 kb IR6 transcript; c) at least one transcript reads through a functional polyadenylation signal; d) some transcripts encoding genes that lie in different reading frames exist as a family of overlapping mRNAs, some in an anti-sense manner. Lastly, of the six Us genes of the EHV-1 KyA strain, only those encoding the EHV-1 protein kinase and the HSV-2 gG/gX homolog are members of the early kinetic class.

Identification and characterization of a cDNA clone derived from the Marek's disease tumour cell line RPL1 encoding a homologue of alpha-transinducing factor (VP16) of HSV-1

We have identified and sequenced a 2.3 kb cDNA clone RPL(N.S) 6 derived from the Marek's disease virus (MDV)-transformed cell line RPL1, which contained open reading frames (ORFs) homologous to UL49 (VP22) and UL48 (VP16) of herpes simplex virus. Northern blot hybridization identified a 2.5 kb transcript corresponding to this cDNA clone in the total RNA from MSB1 lymphoblastoid cells, but not in RNA from the original RPL1 cells, most probably due to the very low level of its transcription. In vitro translation demonstrated that both MDV UL49 and UL48 can be expressed from a single mRNA.

Transduction of foreign regulatory sequences by a replication-defective herpes simplex virus type 1: the rat neuron-specific enolase promoter

Herpes simplex virus type 1 (HSV-1) can transduce genes into non-proliferating cells such as neurons that are refractory to other means of gene transfer. We have been interested to examine the potential usefulness of HSV-1 as a gene transfer vehicle to analyze neuron-specific regulatory sequences. In this study, we have used a replication-defective HSV-1-based vector deleted for the essential immediate early gene 3 (IE3) to transduce a 1.8 kb promoter fragment from the rat neuron-specific enolase gene (nse) linked to the firefly luciferase reporter gene (luc). It has previously been shown that the same promoter fragment is capable of directing neuron-specific expression of a linked reporter gene in transgenic mice. As an internal control for infection and gene expression, we also inserted the chloramphenicol acetyltransferase (cat) gene driven by the SV40 early promoter/enhancer into the thymidine kinase locus of the same vector. We infected (i) non-neuronal BHK-C13 cells which do not express the endogenous nse gene, (ii) differentiated and non-differentiated pheochromocytoma PC12 cells as well as (iii) N1E-115 neuroblastoma cells, all of which do express endogenous nse. All three cell types produced luciferase upon infection, indicating that the same nse promoter fragment that has previously been shown to be regulated in a cell-specific manner in transgenic mice, was not regulated cell type-specifically in the context of the HSV-1 genome.(ABSTRACT TRUNCATED AT 250 WORDS)

Characterization of a Marek's disease virus BamHI-L-specific cDNA clone obtained from a Marek's disease lymphoblastoid cell line

Two Marek's disease (MD) virus BamHI-L-specific cDNA clones were isolated from a cDNA library constructed from poly(A)+ RNA fractions of an MD lymphoblastoid cell line, MDCC-CU41 (CU41). These clones were mapped to the region corresponding to the BamHI-Q2 and L-regions. These clones hybridized with 2.5-, 0.8-, and 0.6-kb transcripts prepared from CU41. The transcriptional unit of the 0.6-kb transcript was determined by RNase protection assays. An open reading frame encoding a 107-amino-acid polypeptide was identified in the 0.6-kb transcript. Reverse transcriptase-PCR demonstrated the presence of this transcript in both CU41 and a reticuloendotheliosis virus-transformed cell line latently infected with MD virus.

Identification of a new transcriptional unit that yields a gene product within the unique sequences of the short component of the herpes simplex virus 1 genome

The herpes simplex virus genome 1 consists of two unique stretches, long (UL) and short (U(S)), each flanked by inverted repeat sequences. The U(S) sequence has been previously reported to contain 12 open reading frames designated U(S)1 through U(S)12. This report demonstrates the existence of a 13th open reading frame within the U(S) sequence, designated U(S)8.5. The U(S)8.5 sequence is located between, and overlaps in part with, the domains of the U(S)8 and U(S)9 genes. Its transcription is initiated within the coding sequence of U(S)8, and its transcript decays earlier than that of U(S)8. On the basis of the size of its RNA (1.2 kb) and map position, it is likely that the U(S)8.5 transcript is 3' coterminal with the U(S)8 and U(S)9 mRNAs at the single polyadenylation signal which serves these genes. The nucleotide sequence of the U(S)8.5 open reading frame predicts that its product is a 151-amino-acid basic, hydrophilic polypeptide. To determine whether the U(S)8.5 encodes a protein, a sequence encoding 23 amino acids that contains an epitope reacting with a known monoclonal antibody to human cytomegalovirus protein was inserted in frame after the predicted fifth codon of the U(S)8.5 gene. The recombinant virus carrying this epitope induced the synthesis of a protein reactive with the monoclonal antibody in immunoblots. The tagged protein localized in nucleoli of cells infected with the recombinant virus.

Regulation of glycoprotein D synthesis of herpes simplex virus 1 by alpha 4 protein, the major regulatory protein of the virus, in stably transformed cell lines: effect of the relative gene copy numbers

Earlier studies concerning gamma 1 gene regulation by the alpha 4 protein, the major regulatory protein of herpes simplex virus 1 (HSV-1), in stably transformed cell lines, reported conflicting results, i.e., alpha 4 protein positively regulated the gamma 1 gB gene in alpha 4/gB cells, while it negatively regulated the gamma 1 gD gene in alpha 4/BJ cells. Both cell lines were derived from a common parental cell line alpha 4/c 113 that contains 1 copy of the alpha 4 gene, and the only apparent difference between them was the relative copy number of the gB and gD sequences (1 and 30-50, respectively) resident in the cell genome. We investigated this disparity by constructing a cell line (BA 4) that contains one copy each of the alpha 4 and gamma 1 gD sequences, by fusion of alpha 4/c 113 and BJt cells, containing and expressing respectively 1 copy of the alpha 4 and gD genes. BA 4 cells constitutively expressed both the alpha 4, gD genes inherited from the parental cell lines (alpha 4/c 113 and BJt). In BA 4 cells that alpha 4 protein positively regulates the gD gene as evidenced from (i) higher levels of gD expression than the parental BJt cells lacking the alpha 4 gene, and (ii) significant decrease in gD expression under conditions that render the alpha 4 protein produced in BA 4 cells non-functional. In addition the gamma 2gG gene contained within the DNA fragment encoding the gD gene, is also expressed in BA 4 cells. On the basis of these data, we propose that gamma gene regulation by the alpha 4 protein is affected by the relative copy number of these genes, resident in the cell genome.

Identification and transcriptional mapping of genes encoded at the IR/Us junction of equine herpesvirus type 1

Two open reading frames (ORFs) encoded at the inverted repeat unique short (Us) junction of the Short (S) region of the equine herpesvirus type 1 genome were identified by DNA sequencing of a 2876 base pair (bp) genomic segment, and transcripts encoding these ORFs were characterized by Northern blot, S1 nuclease, and primer extension analyses. These studies also established the size of each inverted repeat to be 12,768 nucleotides (nts). The IR6 ORF (816 bp), mapping at nts 12,317-11,502 of the S region, is the last gene completely encoded within each inverted repeat and encodes a predicted 30.1-kDa protein of 272 amino acids, which does not exhibit homology to other alphaherpesvirus proteins. IR6 is expressed as an early transcript of 1.2 kb which is detected initially at 1.5 hr p.i. and up to 12 hr p.i. The transcription initiation and termination sites of IR6 were mapped by primer extension and S1 nuclease analyses to nts 12,465 and 11,408, respectively. The first ORF encoded within the Us segment (909 bp; EUS1), mapping at nts 13,397-12,489, encodes a predicted 33.5-kDa protein of 303 amino acids that exhibits 29% identity to the US2 protein of herpes simplex virus 1. EUS1 is expressed as a 2.3-kb mRNA of the gamma-1 class, as its synthesis begins prior to viral DNA replication at 4 hr p.i. but is retarded by phosphonoacetic acid, an inhibitor of viral DNA replication. The Tci and Tct sites of EUS1 were mapped by S1 nuclease analyses to nts 13,637 and 11,408, respectively. Interestingly, this termination site is also utilized by three late mRNAs of 5.8, 3.8, and 1.7 kb which originate within the Us and overlap the IR6 mRNA encoded in the terminal inverted repeat (TR) of the prototype genomic isomer. EUS1 is 3' coterminal with IR6 in the inverted repeat, whereas, the 5.8, 3.8, and 1.7 kb transcripts are 3' coterminal with IR6 of the TR.

Equine herpesvirus 1 glycoprotein D: mapping of the transcript and a neutralization epitope

Studies with molecular and immunological techniques identified and mapped the transcript encoding glycoprotein D (gD) of equine herpesvirus 1 KyA, as well as two continuous gD antigenic determinants. Three mRNA species of 5.5, 3.8, and 1.7 kb overlap the gD open reading frame and are transcribed from the DNA strand encoding gD. Northern (RNA) blot hybridization with both DNA clones and riboprobes, as well as S1 nuclease analyses, showed the 3.8-kb mRNA to encode gD and to be synthesized as a late (beta-gamma) transcript. The 3.8-kb gD mRNA initiates within the US segment 91 and 34 nucleotides downstream of the CCAAT and TATA elements, respectively, and encodes a potential polypeptide of 392 amino acids. The termination site of this transcript maps within the terminal repeat at a site also used by the 5.5-kb mRNA and the IR6-encoded 1.2-kb mRNA, such that these three transcripts form a 3'-coterminal nested set. The extended size (2,250 nucleotides) of the 3' untranslated region of the gD transcript and its termination within the terminal repeat may result from the deletion of 3,859 bp, which eliminates two consensus polyadenylation signals downstream of the gD open reading frame of EHV-1 KyA. Use of antisera to synthetic peptides of 19 amino acids (residues 4 to 22) and 20 amino acids (residues 267 to 285) in Western immunoblot analyses revealed that gD is present in EHV-1 virions as a 55-kDa polypeptide. In addition, these antisera detected the 55-kDa protein as well as 58- and 47-kDa polypeptides in infected-cell extracts at late times of infection. Residues 4 to 22 make up a continuous neutralizing epitope of gD, since incubation of equine herpesvirus 1 with the anti-19-mer serum prior to infection results in reduced numbers of plaques and reduced levels of virus-encoded thymidine kinase. Complement is not required for neutralization mediated by the anti-19-mer serum.

Construction of a US3 lacZ insertion mutant of herpes simplex virus type 2 and characterization of its phenotype in vitro and in vivo

We have constructed and characterized a mutant of herpes simplex virus type 2 (HSV-2) which was inserted a modified lacZ gene, placed under the control of HSV-1 beta 8 promotor, into the US3 protein kinase gene. The mutant, L1BR1, could not induce the virus-encoded protein kinase activity, but could replicate in Vero cells as efficiently as the parental virus. When the biological properties of L1BR1 were examined in mice by using four routes (footpad, intraperitoneal, corneal, and intracerebral) of infection, the mutant displayed the route-dependent reduction of virulence; after inoculation by footpad and intraperitoneal routes, the mutant was more than 10,000-fold less virulent than the parental virus, but it exhibited only about a 10-fold decrease in virulence following the corneal and intracerebral infection. In the intraperitoneal inoculation into adult mice, the replication of L1BR1 in the liver and spleen was severely restricted, but in newborn mice the mutant could grow as well as the parental virus in these organs. The adoptive transfer of peritoneal macrophages from adult mice resulted in a marked inhibition in the replication of L1BR1 in the liver and spleen of newborn mice, while the transfer exhibited little or no effect on the production of the wild-type virus in these organs. We also found that the mutant, unlike the parental virus, could not replicate in precultured peritoneal macrophages from adult mice. Taking these observations together, it seems likely that L1BR1 lost the ability to overcome the mononuclear-phagocytic defense system and thereby lost its pathogenicity by intraperitoneal and footpad routes. Furthermore, the mutant was shown to be rescued by a 4.8-kb HindIII/Xbal fragment containing the entire US3 open reading frame. However, we could not rule out the possibility that some of the phenotypes of L1BR1 are due to mutations in the US3-neighboring genes, US2 and US4.

Activity of the simian virus 40 early promoter-enhancer in herpes simplex virus type 1 vectors is dependent on its position, the infected cell type, and the presence of Vmw175

We have studied some of the parameters governing the expression of a foreign promoter-reporter gene construct incorporated into herpes simplex virus (HSV) type 1. These include the genetic background of the parental virus, the site of transgene insertion within the HSV genome, and the infected cell type. The genetic background of the vector constructs denoted delta 3 was an HSV type 1 mutant deleted for nearly the entire coding portion of Vmw175 (ICP4), the product of the essential immediate-early gene IE3. For vectors denoted +, the IE3 deletion had been repaired by marker rescue. We used as a reporter gene the bacterial chloramphenicol acetyltransferase (CAT) gene, driven by the simian virus 40 (SV40) early promoter and enhancer region. The SV40-cat hybrid gene was inserted either into the HSV thymidine kinase (TK) locus to create the vectors TKScat delta 3 and TKScat+ or into an intergenic site within the BamHI z fragment of the short unique portion of the viral genome to create the vectors GScat delta 3 and GScat+. In Vero and BHK cells infected with TKScat delta 3, CAT activity was first detected at 10 h postinfection and continued to accumulate until 36 h postinfection. In cells of primate origin infected with the replication-competent vector TKScat+, or in primate cells which complement the IE3 deficiency and which were infected with TKScat delta 3, CAT activity was significantly lower than in cells of rodent origin. However, levels of CAT were increased in the presence of cycloheximide, suggesting that the low production of CAT in primate cells was due to repression of SV40-cat hybrid gene expression. In contrast with results with TKScat delta 3 and TKScat+, CAT activity was not detectable in any of the tested cell types infected with GScat delta 3 or GScat+ except under conditions of cycloheximide reversal. These results show that while HSV gene products expressed in the presence of Vmw175 inhibited SV40-cat expression in the tk locus in a cell-type-specific manner, HSV gene products expressed in the presence or absence of Vmw175 inhibited SV40-cat expression in the BamHI z locus independently of cell type.

The herpes simplex virus 1 protein kinase encoded by the US3 gene mediates posttranslational modification of the phosphoprotein encoded by the UL34 gene

Earlier studies have shown that a herpes simplex virus 1 (HSV-1) open reading frame, US3, encodes a novel protein kinase and have characterized the cognate amino acid sequence which is phosphorylated by this enzyme. This report identifies an apparently essential viral phosphoprotein whose posttranslational processing involves the viral protein kinase. Analyses of viral proteins phosphorylated in the course of productive infection revealed a phosphoprotein whose mobility was viral protein kinase and serotype dependent. Thus, the corresponding HSV-1 and HSV-2 phosphoproteins differ in their electrophoretic mobilities, and the phosphoprotein specified by the HSV-1 mutant deleted in US3 (R7041) differs from that of the corresponding HSV-1 and HSV-2 proteins. Analyses of HSV-1 x HSV-2 recombinants mapped the phosphoprotein between 0.42 and 0.47 map units on the prototype HSV-1 DNA map. Within this region, the UL34 open reading frame was predicted to encode a protein of appropriate molecular weight which would also contain the consensus target site for phosphorylation by the viral protein kinase as previously defined with synthetic peptides. Replacement of the native UL34 gene with a UL34 gene tagged with a 17-amino-acid epitope from the alpha 4 protein identified this gene as encoding the phosphoprotein. Finally, mutagenesis of the predicted phosphorylation site on UL34 in the viral genome, and specifically the substitution of threonine or serine with alanine in the product of the UL34 gene, yielded phosphoproteins whose electrophoretic mobilities could not be differentiated from that of the US3- mutant. We conclude that the posttranslational processing of the UL34 gene product to its wild-type phenotype requires the participation of the viral protein kinase. While the viral protein kinase is not essential for viral replication in cells in culture, the UL34 gene product itself may not be dispensable.

Identification and comparative sequence analysis of a gene in equine herpesvirus 1 with homology to the herpes simplex virus glycoprotein D gene

A homologue of the herpes simplex virus (HSV) glycoprotein D gene has been identified in the genome of equine herpesvirus-1 (EHV-1, equine abortion virus). An open reading frame in the middle of the short unique (US) region is capable of encoding a polypeptide of 402 amino acids that has 26% and 20% of its residues matching pseudorabies virus (PRV) gp50 and HSV-1 gD, respectively. Despite this low level of similarity, the positional identity of six cysteine residues and certain motifs, and the location of the EHV-1 gene, clearly define the EHV-1 polypeptide as one of a family of "gD-like" proteins. Two transcripts of 3.3-3.6 kb and 5.4-5.9 kb were identified, consistent with coterminal mRNAs for the EHV-1 gD gene and the adjacent upstream gene, respectively. Partial sequencing of other regions in US also revealed EHV-1 homologues of HSV-1 gE and gI genes, and a possible equivalent gene to PRV gX. By analogy with the ability of HSV-1 gD and PRV gp50 to induce strong anti-viral immune responses, the EHV-1 gD gene product is expected to be an excellent candidate for development as a vaccine antigen.

The relative stability of selected herpes simplex virus type 1 mRNAs

The relative stability of herpes simplex virus type 1 mRNAs was investigated by examination of the decay rates of selected viral transcripts. The synthesis of mRNA was inhibited by the addition of dactinomycin to HSV-1 infected cells, and the abundance of individual transcripts was determined at subsequent times by RNA blot hybridization. For two immediate-early mRNAs, those encoding the 110 and 63 kilodalton immediate-early proteins, RNA synthesis was inhibited at 3 h post-infection and mRNA half-lives of 5-7 h were found. Examination at 5 h post-infection of the early mRNA encoding thymidine kinase as well as the late mRNA encoding glycoprotein H revealed half-lives of 8-11 h. In contrast, at 12 h post-infection, the late mRNAs encoding the glycoproteins C, E, as well as H were found to have half-lives of 14-29 h. These findings suggest that the relative stability of viral mRNA increases late in infection and is dependent upon the time after infection rather than being strictly a property of the mRNA itself.

Organization and function of the ORIs sequence in the genome of EHV-1 DI particles

Equine herpesvirus type 1 (EHV-1) cultures enriched for defective interfering particles (DIP) mediate oncogenic transformation and persistent infection in permissive hamster embryo fibroblasts. We have recently demonstrated that an origin of replication (ORI) is located within the central portion (map units 0.828 and 0.948) of the inverted repeat sequence (IRs) of the short region of the standard EHV-1 genome. In the generation of the genome of EHV-1 DI particles, sequences from this internal portion of the IRs recombine with sequences at the long region terminus at nucleotides 3244-3251. In this paper we report that the ORIs sequence is precisely conserved in the DIP genome, that direct repeat sequences near the ORIs sequence which may enhance DNA replication are mutated in the DIP genome, and that the ORI sequence of DIP DNA is functional in DNA replication assays.

Weight matrix descriptions of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences

Optimized weight matrices defining four major eukaryotic promoter elements, the TATA-box, cap signal, CCAAT-, and GC-box, are presented; they were derived by comparative sequence analysis of 502 unrelated RNA polymerase II promoter regions. The new TATA-box and cap signal descriptions differ in several respects from the only hitherto available base frequency Tables. The CCAAT-box matrix, obtained with no prior assumption but CCAAT being the core of the motif, reflects precisely the sequence specificity of the recently discovered nuclear factor NY-I/CP1 but does not include typical recognition sequences of two other purported CCAAT-binding proteins, CTF and CBP. The GC-box description is longer than the previously proposed consensus sequences but is consistent with Sp1 protein-DNA binding data. The notion of a CACCC element distinct from the GC-box seems not to be justified any longer in view of the new weight matrix. Unlike the two fixed-distance elements, neither the CCAAT- nor the GC-box occurs at significantly high frequency in the upstream regions of non-vertebrate genes. Preliminary attempts to predict promoters with the aid of the new signal descriptions were unexpectedly successful. The new TATA-box matrix locates eukaryotic transcription initiation sites as reliably as do the best currently available methods to map Escherichia coli promoters. This analysis was made possible by the recently established Eukaryotic Promoter Database (EPD) of the EMBL Nucleotide Sequence Data Library. In order to derive the weight matrices, a novel algorithm has been devised that is generally applicable to sequence motifs positionally correlated with a biologically defined position in the sequences. The signal must be sufficiently over-represented in a particular region relative to the given site, but need not be present in all members of the input sequence collection. The algorithm iteratively redefines the set of putative motif representatives from which a weight matrix is derived, so as to maximize a quantitative measure of local over-representation, an optimization criterion that naturally combines structural and positional constancy. A comprehensive description of the technique is presented in Methods and Data.

Short, duplicated sequence indicative of the recombinogenicity of the junction between a unique and an inverted repeat sequence in the S component of the herpes simplex virus type 1 genome

A herpes simplex virus type 1 (HSV-1) strain, B3, was found to have a short duplication on the left junction between the unique sequence (US) and the inverted repeat sequence (RS) in the S component of the genome DNA. A short region of RS contiguous to the left US-RS junction was duplicated in B3. Based on the nucleotide sequences in and around the US-RS junctions of B3 and other HSV-1 strains, a concept of junction stretch was proposed. The organization of junction stretch is RS side 5'-(G or A stretch)AGC-3' US side. Introduction of the concept of junction stretch led to a definition of the structure in and around the US-RS junction, in the form common to HSV-1 strains. The right end of US in the HSV-1 genome was the A of the ATG initiation codon of gene US12, and thus the ATG triplet may act as a buffer to prevent expansion of RS, as is the case with HSV-2. The duplication in B3 was generated by a crossover event between a point on RS and the US side end of the left junction stretch. These observations suggest that the US side end of the junction stretch possesses the property of recombinogenicity, responsible for generation of the duplication in strain B3 and also for the formation of the US-RS junction of HSV.

Expression of herpes simplex virus type 1 latency-associated transcripts in the trigeminal ganglia of mice during acute infection and reactivation of latent infection

Herpes simplex virus type 1 (HSV-1) establishes a latent infection in the trigeminal ganglia of mice infected via the eye. In these ganglia three viral transcripts, of 2.0, 1.5, and 1.45 kilobases (kb), which are at least partially colinear, have been identified by Northern (RNA) blot analysis. These RNAs partially overlap ICPO, but are transcribed in the opposite direction (J. G. Spivack and N. W. Fraser, J. Virol. 61:3841-3847, 1987). The accumulation of these latency-associated transcripts, as well as other viral RNAs, was studied during an acute infection and the reactivation of a latent HSV-1 infection in mice. The 2.0-kb latency-associated transcript was detected in trigeminal ganglia of mice as early as 4 days postinfection, and the 1.45- and 1.5-kb RNA doublet was detected at 14 days postinfection. The levels of these latency-associated transcripts increased steadily over a 60-day period. In contrast, other HSV-1 transcripts were detected at 2 to 3 days postinfection, reached a peak on day 4, and rapidly declined below detectable levels by day 7. The data indicate that the temporal expression of the latency-associated genes during acute infection in the trigeminal ganglia of mice is different from the temporal expression of genes involved in HSV-1 replication. During the reactivation of latent HSV-1 from explanted trigeminal ganglia, the latency-associated RNAs decreased about twofold, but were present at significant levels even after HSV-1 DNA increased and infectious virus was recovered. The decrease of the latency-associated transcripts occurred when reactivation was blocked by phosphonoacetic acid or novobiocin, which suggests that this decrease may be an early event in the entry of latent HSV-1 into the viral replication cycle.

Regulation of glycoprotein D synthesis: does alpha 4, the major regulatory protein of herpes simplex virus 1, regulate late genes both positively and negatively?

Earlier studies have described the alpha 4/c113 baby hamster kidney cell line which constitutively expresses the alpha 4 protein, the major regulatory protein of herpes simplex virus 1 (HSV-1). Introduction of the HSV-1 glycoprotein B (gB) gene, regulated as a gamma 1 gene, into these cells yielded a cell line which constitutively expressed both the alpha 4 and gamma 1 gB genes. The expression of the gB gene was dependent on the presence of functional alpha 4 protein. In this article we report that we introduced into the alpha 4/c113 and into the parental BHK cells, the HSV-1 BamHI J fragment, which encodes the domains of four genes, including those of glycoproteins D, G, and I (gD, gG, and gI), and most of the coding sequences of the glycoprotein E (gE) gene. In contrast to the earlier studies, we obtained significant constitutive expression of gD (also a gamma 1 gene) in a cell line (BJ) derived from parental BHK cells, but not in a cell line (alpha 4/BJ) which expresses functional alpha 4 protein. RNA homologous to the gD gene was present in significant amounts in the BJ cell line; smaller amounts of this RNA were detected in the alpha 4/BJ cell line. RNA homologous to gE, presumed to be polyadenylated from signals in the vector sequences, was present in the BJ cells but not in the alpha 4/BJ cells. The expression of the HSV-1 gD and gE genes was readily induced in the alpha 4/BJ cells by superinfection with HSV-2. The BJ cell line was, in contrast, resistant to expression of HSV-1 and HSV-2 genes. The BamHI J DNA fragment copy number was approximately 1 per BJ cell genome equivalent and 30 to 50 per alpha 4/BJ cell genome equivalent. We conclude that (i) the genes specifying gD and gB belong to different viral regulatory gene subsets, (ii) the gD gene is subject to both positive and negative regulation, (iii) both gD and gE mRNAs are subject to translational controls although they may be different, and (iv) the absence of expression of gD in the alpha 4/BJ cells reflects the expression of the alpha 4 protein in these cells.

Detection of herpes simplex virus type 1 transcripts during latent infection in mice

A latent infection can be established in the trigeminal ganglia of mice after corneal inoculation of herpes simplex virus type 1 (HSV-1). With a virion DNA probe, three transcripts (2.0, 1.5, and 1.45 kilobases [kb]) were detected by Northern blot (RNA blot) analysis of RNAs isolated from the ganglia of latently infected mice. All three transcripts hybridized to a nick-translated HSV-1 DNA probe from BamHI restriction fragment B (strain F). These RNAs were mapped with subfragments of BamHI-B and with strand-specific probes. They are at least partially colinear with each other, map to a 3.0-kb PstI-MluI subfragment of BamHI-B, and are transcribed from left to right. The latent HSV-1 RNAs partially overlap the 3' end of ICP0 mRNA but are transcribed in the opposite direction. The latent RNAs were not as extensively poly(A)+ as actin mRNA. The HSV-1 transcripts detected in latently infected trigeminal ganglia did not correspond with any that have been previously identified in permissively infected cells in tissue culture. However, the 2.0-kb HSV-1 RNA present during latency was detectable at reduced levels in the trigeminal ganglia of acutely infected mice and in infected tissue culture cells. The data indicate that the pattern of viral gene expression during HSV-1 latency in the trigeminal ganglia of mice does not represent restriction of the genes actively transcribed during the lytic replication cycle in tissue culture.

Rapid identification of nonessential genes of herpes simplex virus type 1 by Tn5 mutagenesis

The large genome of herpes simplex virus type of (HSV-1) encodes at least 80 polypeptides, the majority of which have no recognized function. A subgroup of these gene products appears to be nonessential for virus replication in cell culture, but contributes to the complex life cycle of the virus in the host. To identify such functions, a simple insertional mutagenesis method has been used for selective inactivation of individual HSV-1 genes. The bacterial transposon Tn5 was allowed to insert randomly into cloned restriction fragments representing the entire short unique (US) region of the HSV-1 genome. Of the 12 open reading frames that were mutagenized with Tn5, mutant derivatives of US2, US4, and US5 were recombined into the virus. These three genes proved to be nonessential for HSV-1 replication in Vero (African Green monkey kidney) cells and the US4 gene appeared to be involved in viral pathogenesis in the central nervous system of mice. This rapid mutagenesis procedure should prove useful in exploring the entire HSV-1 genome as well as the genomes of other complex animal viruses.

Characterization and nucleotide sequence of two herpes simplex virus 1 genes whose products modulate alpha-trans-inducing factor-dependent activation of alpha genes

Herpes simplex viruses encode a structural protein which induces, in trans, expression of alpha genes, the first set of genes to be expressed after infection of permissive cells. This protein, designated as the alpha-trans-inducing factor (alpha-TIF), maps within the BamHI F fragment, and its gene has been sequenced. In the course of mapping the domain of the alpha-TIF gene, it was noted that the intact BamHI fragment was consistently more effective than the complete domain of the alpha-TIF gene in inducing expression of alpha genes. Cotransfections of DNA fragments containing an alpha indicator gene and the alpha-TIF gene with various regions of the BamHI F DNA fragment revealed that the sequences located 3' to the alpha-TIF gene raised the activity of the alpha-TIF gene to nearly the same level as that of the intact BamHI F fragment. The nucleotide sequence and S1 nuclease mapping analyses revealed the presence of two transcribed open reading frames capable of encoding polypeptides with translated molecular weights of 77,357 and 70,527. To determine whether the effect of these sequences in trans on alpha-TIF-mediated induction of alpha genes was due to expression of these genes or competition for transcriptional factors, we constructed plasmids that contained both genes. Into each or both of these genes we inserted, near the translation initiation sites, 14-base-pair linkers carrying translational stop codons (TAG) in all three reading frames. Analyses of these plasmids indicated that the gene encoding the 70,527-molecular-weight polypeptide reduced alpha-TIF-dependent induction of alpha genes, whereas the gene encoding the 77,357-molecular-weight polypeptide increased this activity. Insertion of the stop codons abolished these activities.

Transcription initiation sites and nucleotide sequence of a herpes simplex virus 1 gene conserved in the Epstein-Barr virus genome and reported to affect the transport of viral glycoproteins

Earlier reports have localized mutations which affect the processing and transport of herpes simplex virus 1 glycoproteins to a region located between the genes specifying glycoprotein B and the major viral DNA-binding protein (beta 8). The nucleotide sequence of this region contains a single long open reading frame encoding a 780-amino-acid protein with a predicted molecular weight of 83,845. To confirm the existence of this protein, rabbit polyclonal antibody was made against a synthetic peptide made according to the predicted sequence of a hydrophilic domain near the carboxy terminal of the protein. This antibody reacted with an infected cell protein of an apparent molecular weight of 95,500. We designated this protein infected cell protein 18.5 (ICP18.5). S1 nuclease analysis suggested that the 5.6-kilobase mRNA encoding ICP18.5 is initiated predominantly from one site, but three weaker initiation sites also seemed to occur within a 74-base-pair stretch of DNA. This gene appears to be conserved in the Epstein-Barr virus (EBV) genome, inasmuch as 174 of the 780 amino acids of ICP18.5 align with corresponding amino acids predicted by the EBV open reading frame BALF3. The EBV gene is located adjacent to the gene specifying a homolog of the herpes simplex virus 1 glycoprotein B.

Regulation of transcription in vitro from herpes simplex virus genes

In vitro transcription assays were carried out by using as templates DNAs cut from the herpes simplex virus early glycoprotein D gene, the late glycoprotein C gene, the late VP5 gene, and the immediate-early ICP22 gene. Nuclear extracts from suspension cultures of uninfected HeLa cells effectively synthesized RNAs from genes of the immediate-early and delayed-early classes. To a lesser extent, the extracts also used DNAs cut from the late genes as templates. Transcription from the immediate-early gene was inhibited in extracts prepared from infected cells. Analysis of the proteins in infected-cell extracts by gel electrophoresis, transfer to nitrocellulose, and probing with specific antibody demonstrated the presence of the viral regulatory protein ICP4. Chromatographic fractionation of nuclear extract from infected cells yielded a mixture of proteins (fraction VIII) enriched in ICP4 (S.W. Faber and K.W. Wilcox, Nucleic Acids Res., 14:6067-6083, 1986). Addition of fraction VIII to the in vitro assay affected transcription. Depending on the DNA in the assay, an inhibitory or stimulatory effect was observed. Inhibition of RNA synthesis was found when DNA from the immediate-early gene was used as a template, and stimulation was found when DNA from the early or late gene was used.

Sequence of the short unique region, short repeats, and part of the long repeats of human cytomegalovirus

We have determined the DNA sequence (46 kilobases) of the short unique region, the short repeat, and part of the long repeat of human cytomegalovirus strain AD169. Analysis of the sequence has revealed at least 38 possible regions that may code for protein. Many of these open reading frames show homology to each other, and five groups of homologous reading frames are identified. Half of the predicted translation products appear to be membrane proteins, and fall into two distinct classes; those that have potential signal and anchor sequences, and those that have seven potential membrane-spanning regions and appear to be integral membrane proteins. A number of the former class contain sites for N-linked glycosylation and may therefore be glycoproteins. None of the 38 open reading frames shows homology to other known herpesvirus proteins.

The herpes simplex virus type 2 equivalent of the herpes simplex virus type 1 US7 gene and its flanking sequences

Nucleotide sequencing studies (D. J. McGeoch, A. Dolan, S. Donald, and F. Rixon, 1985, J. Mol. Biol. 181, 1-14) have indicated that herpes simplex virus type 1 (HSV-1) has a coding sequence, referred to as US7, between the genes for the glycoproteins D and E (gD and gE). Northern blot analysis and nucleotide sequencing have been carried out to show that the type 2 virus (HSV-2) has an equivalent to the US7 gene. A comparison with the HSV-1 sequence has revealed some surprising similarities and differences. At the nucleotide level, HSV-2 has inserted a large sequence into the gE promoter, retained a large palindrome present in the coding sequence but not some tandem repeats, and deleted a region beside those repeats. At the amino acid level, the putative transmembrane sequence has been remarkably well conserved, and hydrophobic moment analysis indicates that it could be interacting with polar species within the plane of the membrane. Immediately after the deletion in the HSV-2 sequence, there is an N-glycosylation signal, and HSV-2 has one more such signal than HSV-1. The longest conserved sequence at the nucleotide level codes for a region of polypeptide that is strongly predicted to fold into alpha-helix. Implications of these analyses to the structure and possible function of these molecules are discussed.

The 10K virion phosphoprotein encoded by gene US9 from herpes simplex virus type 1

Gene US9 of herpes simplex virus type 1 has been predicted, from DNA sequence analysis, to encode a protein of mol wt 10,026, designated 10K (D.J. McGeoch, A. Dolan, S. Donald, and F.J. Rixon (1985). J. Mol. Biol. 181, 1-13). We have investigated this protein by using a synthetic peptide corresponding to the 11 amino acids adjacent to the amino-terminal methionine and rasing antisera in rabbits. One antiserum was able to precipitate at least 12 electrophoretically distinct polypeptide species from extracts of BHK cells infected with HSV-1. The estimated molecular weights of these polypeptides ranged from 12K to 20K and immunoblotting showed them to be related proteins. The primary translation product has an apparent mol wt of 13K. The various forms of 10K differ in their relative abundance in the infected cell and also in their degree of phosphorylation. Lower molecular weight forms of the 10K protein can be precipitated from NP-40 extracts of HSV-1 virions, suggesting that these forms of 10K are contained in the virion tegument or envelope. An association between this protein and nucleocapsids has also been observed in the nuclei of infected cells by immunoelectron microscopy. These observations imply that the product of US9 is a tegument protein which becomes associated with nucleocapsids at, or soon after, their formation in the nuclei of infected cells.

Alphaherpesviruses possess a gene homologous to the protein kinase gene family of eukaryotes and retroviruses

The US3 genes of herpes simplex virus serotypes 1 and 2, and the corresponding gene of varicella-zoster virus, encode proteins whose sequences are clearly homologous to members of the protein kinase family of eukaryotes and retroviruses. Similarity is most characteristic, and strongest, in an 80 residue region comprising part of the catalytic structure of the kinases. In this region the herpesvirus proteins are most like a yeast cell division control protein, and least like the retrovirus protein-tyrosine kinases. We consider that the herpesvirus proteins are probably involved in modulation of cellular processes during lytic infection, although other roles are also possible, for example in latent infection.

Identification of a new glycoprotein of herpes simplex virus type 1 and genetic mapping of the gene that codes for it

A type-specific monoclonal antibody, LP10, precipitated a glycoprotein with a molecular weight of approximately 59,000 from purified herpes simplex virus type 1. Although this glycoprotein was similar in size to glycoprotein D (gD), it was shown to be less abundant in both virions and infected cells, to migrate more rapidly in its precursor form, to incorporate glucosamine but not mannose, and to have a more stable precursor in tunicamycin-treated cells than the gD precursor (pgD). Immunoassays of cells infected with insertion recombinants and intertypic recombinants localized the gene coding for the target antigen of LP10 to the unique short (Us) region at map units 0.892 to 0.924 excluding gD. The target antigen of LP10 was then definitively mapped to the Us4 open reading frame by immunoprecipitation of a polypeptide synthesized by in vitro translation of a Us4-specific transcript prepared by using an SP6 cloning This newly identified glycoprotein product of the Us4 gene of herpes simplex virus type 1 is distinct from the previously identified gB1, gC1, gE1, and gH1.

On the predictive recognition of signal peptide sequences

DNA sequence analysis of the short unique regions in the genomes of herpes simplex virus (HSV), types 1 and 2, has previously shown that within this region there are four genes, designated US2, US4, US5 and US7, whose functions are unknown but whose predicted amino sequences exhibit hydrophobic N-termini (D.J. McGeoch et al., 1985, J. Mol. Biol. 181, 1-13; D.J. McGeoch, H.W.M. Rixon and D. McNab, unpublished data). In this paper, the possibility was investigated that these hydrophobic sequences might be signal sequences associated with membrane-bound translation of the proteins, and subsequent secretion or insertion into membranes. By using reference sets of protein sequences known to be translated either on membrane-bound or on free ribosomes, criteria were developed to distinguish between these two classes. These criteria comprised: length and net charge of the immediately N-terminal region which often precedes the hydrophobic stretch in membrane-translated proteins; length of the uncharged (hydrophobic) region; and degree of hydrophobicity of the 8-residue maximal hydrophobic region. The latter two parameters were found to be particularly effective when combined as a two dimensional plot, which clearly distinguished 96% of membrane-translated proteins from other classes. When the uncharacterized, predicted HSV protein sequences were judged by these tests, it was found that the products of genes US4, US5 and US7 were convincingly classified as membrane-translated, while the US2 product gave a less definitive result. In conclusion, the US4, US5 and US7 gene products were considered probably to be previously unrecognized, virion membrane-inserted glycoproteins.