Characterization of RNA transcripts from herpes simplex virus-1 DNA fragment BamHI-B

HSV1 latent transcription and non-coding RNA: A critical retrospective

Virologists have invested great effort into understanding how the herpes simplex viruses and their relatives are maintained dormant over the lifespan of their host while maintaining the poise to remobilize on sporadic occasions. Piece by piece, our field has defined the tissues in play (the sensory ganglia), the transcriptional units (the latency-associated transcripts), and the responsive genomic region (the long repeats of the viral genomes). With time, the observed complexity of these features has compounded, and the totality of viral factors regulating latency are less obvious. In this review, we compose a comprehensive picture of the viral genetic elements suspected to be relevant to herpes simplex virus 1 (HSV1) latent transcription by conducting a critical analysis of about three decades of research. We describe these studies, which largely involved mutational analysis of the notable latency-associated transcripts (LATs), and more recently a series of viral miRNAs. We also intend to draw attention to the many other less characterized non-coding RNAs, and perhaps coding RNAs, that may be important for consideration when trying to disentangle the multitude of phenotypes of the many genetic modifications introduced into recombinant HSV1 strains.

Mammalian alphaherpesvirus miRNAs

Mammalian alphaherpesviruses are major causes of human and veterinary disease. During productive infection, these viruses exhibit complex and robust patterns of gene expression. These viruses also form latent infections in neurons of sensory ganglia in which productive cycle gene expression is highly repressed. Both modes of infection provide advantageous opportunities for regulation by microRNAs. Thus far, published data regarding microRNAs are available for six mammalian alphaherpesviruses. No microRNAs have yet been detected from varicella zoster virus. The five other viruses-herpes simplex viruses-1 and -2, herpes B virus, bovine herpesvirus-1, and pseudorabies virus-representing both genera of mammalian alphaherpesviruses have been shown to express microRNAs. In this article, we discuss these microRNAs in terms of where they are encoded in the viral genome relative to other viral transcripts; whether they are expressed during productive or latent infection; their potential targets; what little is known about their actual targets and functions during viral infection; and what little is known about the interactions of these viruses with the host microRNA machinery. This article is part of a Special Issue entitled: "MicroRNAs in viral gene regulation".

A mutant deleted for most of the herpes simplex virus type 1 (HSV-1) UOL gene does not affect the spontaneous reactivation phenotype in rabbits

The mechanisms involved in the herpes simplex virus type 1 (HSV-1) latency-reactivation cycle are not fully understood. The latency-associated transcript (LAT) is the only HSV-1 RNA abundantly detected during neuronal latency. LAT plays a significant role in latency because LAT(-) mutants have a reduced reactivation phenotype. Several novel viral transcripts have been identified within the LAT locus, including UOL, which is located just upstream of LAT. The authors report here on a mutant, DeltaUOL, which has a 437-nucleotide deletion that deletes most of UOL. DeltaUOL replicated similarly to its wild-type parental McKrae HSV-1 strain in infected cells, the eyes, trigeminal ganglia, and brains of mice and rabbits. It was indistinguishable from wild-type virus as regards explant-induced reactivation in mice, and spontaneous reactivation in rabbits. In contrast, DeltaUOL was significantly less virulent in mice. Thus, UOL appears to be dispensable for the wild-type reactivation phenotype while appearing to play a role in neurovirulence in ocularly infected animals.

Identification of a protein encoded in the herpes simplex virus type 1 latency associated transcript promoter region

Herpes simplex virus type 1 (HSV-1) establishes a lifelong latency in the neurons of its host. Sporadically, the latent virus reactivates and spreads back to the original site of infection and causes recrudescent diseases. The only gene actively transcribed during neuronal latency is the latency associated transcript (LAT) gene. Several transcripts have been detected in the important LAT promoter region. However, no polypeptides coded by these transcripts are known. In this communication, we reported the cloning, sequencing, and characterization of a transcript immediately upstream of LAT. We designated this gene UOL (Upstream of LAT). The UOL RNA is polyadenylated, expressed as a late gene in infected cells, transcribed in the same direction as LAT, and contains an open reading frame (ORF) capable of encoding a protein of 96 amino acids with a predicted molecular mass of 11 kDa. The UOL transcript contains 466 nucleotides in length. The 5' end of the UOL transcript starts at nucleotide 118,266 and the 3' end of the UOL transcript ends at nucleotide 118,731 based on the published 17syn+ genomic sequence. The UOL protein was detected in infected cell lysates by immunoprecipitation using an antibody raised against UOL ORF synthetic peptide. More importantly, sera from mice infected with wild-type HSV-1 but not sera from mice infected with a mutant with the UOL region deleted recognized the UOL ORF, expressed in Escherichia coli, on Western blots. These results suggest that a UOL protein is in HSV-1 infected tissue culture cells and in mice infected with HSV-1.

Immune responses to replication-defective HSV-1 type vectors within the CNS: implications for gene therapy

Herpes simplex virus (HSV) is a naturally occurring double-stranded DNA virus that has been adapted into an efficient vector for in vivo gene transfer. HSV-based vectors exhibit wide tropism, large transgene size capacity, and moderately prolonged transgene expression profiles. Clinical implementation of HSV vector-based gene therapy for prevention and/or amelioration of human diseases eventually will be realized, but inherently this goal presents a series of significant challenges, one of which relates to issues of immune system involvement. Few experimental reports have detailed HSV vector-engendered immune responses and subsequent resolution events primarily within the confines of the central nervous system. Herein, we describe the immunobiology of HSV and its derived vector platforms, thus providing an initiation point from where to propose requisite experimental investigation and potential approaches to prevent and/or counter adverse antivector immune responses.

Global analysis of herpes simplex virus type 1 transcription using an oligonucleotide-based DNA microarray

More than 100 transcripts of various abundances and kinetic classes are expressed during phases of productive and latent infections by herpes simplex virus (HSV) type 1. To carry out rapid global analysis of variations in such patterns as a function of perturbation of viral regulatory genes and cell differentiation, we have made DNA microchips containing sets of 75-mer oligonucleotides specific for individual viral transcripts. About half of these are unique for single transcripts, while others function for overlapping ones. We have also included probes for 57 human genes known to be involved in some aspect of stress response. The chips efficiently detect all viral transcripts, and analysis of those abundant under various conditions of infection demonstrates excellent correlation with known kinetics of mRNA accumulation. Further, quantitative sensitivity is high. We have further applied global analysis of transcription to an investigation of mRNA populations in cells infected with a mutant virus in which the essential immediate-early alpha27 (U(L)54) gene has been functionally deleted. Transcripts expressed at 6 h following infection with this mutant can be classified into three groups: those whose abundance is augmented (mainly immediate-early transcripts) or unaltered, those whose abundance is somewhat reduced, and those where there is a significant reduction in transcript levels. These do not conform to any particular kinetic class. Interestingly, levels of many cellular transcripts surveyed are increased. The high proportion of such transcripts suggests that the alpha27 gene plays a major role in the early decline in cellular gene expression so characteristic of HSV infection.

Identification of a novel 0.7-kb polyadenylated transcript in the LAT promoter region of HSV-1 that is strain specific and may contribute to virulence

Herpes Simplex virus expresses latency-associated transcripts (LATs) the function of which remains obscure despite increasing knowledge of their structure and expression. Upstream of the LAT coding region is a region of the genome that is poorly characterized although it lies in an area that is responsible for modulation of reactivation efficiency in two different animal models. Transcript mapping with strains 17, McKrae, KOS, and F has revealed strain differences in this region of the viral genome. Strain 17 and McKrae expressed a novel polyadenylated 0.7-kb transcript that is absent from KOS and F. This transcript is expressed in the LAT direction and has the kinetics of a true late gene during the lytic cycle of infection. A deletion mutant, 17DeltaBsa, which does not express the 0.7-kb RNA, is less virulent than the parental strain 17. A rescuant with F sequence (17DeltaBsa/RF) shows virulence similar to F, whereas a rescuant with strain 17 sequence (17DeltaBsa/R17) is similar to strain 17. Virulence is altered by deletion or substitution in the region encoding the 0.7-kb transcript (BsaI-BsaI); however, reactivation in the mouse explant cocultivation assay or the adrenergically induced rabbit reactivation model remained unchanged. The importance of this region for virulence is discussed.

HSV type 1 genome variants from persistently productive infections in Raji and BJAB cell lines

We studied possible genomic changes occurring in herpes simplex virus type 1 (HSV-1) during long-term cell culture which served as a model system for persistence and latency studies as introduced earlier. Sixteen HSV-1 reisolates were isolated from persistently productive HSV-1 (strains F and AK)-infected Burkitt lymphoma cell lines Raji and BJAB at four different times. They were roughly characterized in plaque morphology, plaque size, and infectivity. The viral reisolate DNAs revealed deletions and insertions of up to 1,150 base pairs in fragments BamHI-B, -E, -F, -J, -V, -X, and in the L-terminal and junction fragments S and K. Results were confirmed by additional restriction enzyme analyses and DNA sequencing of selected genomic regions between map units 0.642-0.650, 0.763-0.778 and 0.887-0.934. There was a progressive increase in genomic variability over a three-year period. However, changes in DNA fragment size occurred at different rates, with some reisolates showing stability over several months. The selective pressure for HSV-1 (F and AK) genomic changes was stronger in Raji than in BJAB cells, and stronger for F than for AK strain.

Herpes simplex virus type 1 (HSV-1) UL56 gene is involved in viral intraperitoneal pathogenicity to immunocompetent mice

A comparison of the pathogenicity in mice of the recombinant herpes simplex virus type 1 (HSV-1) strain HSV-1-M-LacZ, in which the UL56 gene has been deleted, was made with its parental strain F, following infection in different mouse strains. The polymerase chain reaction (PCR) technique was used to study the migration of virus DNA in the mouse model. Tissues from adult mice infected intraperitoneally (IP) with one of three HSV-1 strains (F, HFEM or HSV-1-LacZ) were examined for the presence of viral DNA. DNA of the pathogenic strain F was detected in the adrenal glands, spinal cord, brain, liver and pancreas. DNA of HSV-1-M-LacZ was detected in the same tissues. However, DNA of the apathogenic strain HFEM was detected transiently (on days 2 and 3 p.i., but not days 1, 5 or 7), only in the adrenal glands and no viral DNA was detected in any of the other tissues. HSV-1 pathogenic strains injected intraperitoneally into newborn mice (7 days old) killed most of the mice. In the surviving mice viral DNA of the three virus strains was found in peritoneal exudate cells (PEC), adrenal glands, spinal cord, liver and spleen. It was found that HSV-1-M-LacZ, which lacks the UL56 gene, resembled in pathogenicity to the newborn mice the pathogenic HSV-1 strains F and KOS. The PCR technique was used to trace viral DNA in tissues of the mice which survived HSV-1 infection at 7 weeks of age. Only HSV-1 (KOS) DNA was detected in the pancreas. The brains of these mice did not contain viral DNA. It is suggested that HSV-1 DNA may reside in surviving HSV-1- infected newborn mice in a "latent" state in nonneural tissues.

Open reading frames in a 4556 nucleotide sequence within MDV-1 BamHI-D DNA fragment: evidence for splicing of mRNA from a new viral glycoprotein gene

A DNA segment of the MDV-1 BamHI-D fragment was sequenced, and the open reading frames (ORFs) present in the 4556 nucleotide fragment were analyzed by computer programs. Computer analysis identified 19 putative ORFs in the sequence ranging from a coding capacity of 37 amino acids (aa) (ORF-1a) to 684aa (ORF-1). The special properties of four ORFs (1a, 1, 2, and 3) were investigated. Two adjacent ORFs, ORF-1a and ORF-1, were found by computer analysis to have the properties of two introns encoding a glycoprotein: ORF-1a encodes an aa sequence with the properties of a signal peptide, and ORF-1 encodes a polypeptide with a membrane anchor domain and putative N-glycosylation sites in the aa sequence. ORF-1a and ORF-1 were found to be transcribed in MDV-1-infected cells. Two RNA transcripts were detected: a precursor RNA and its spliced form. Both are transcribed from a promoter located 5' to ORF-1a, and splice donor and acceptor sites are used to splice the mRNA after cleavage of a 71-nucleotide sequence. This finding suggest that ORF-1a and ORF-1 are two introns of a new MDV-1 glycoprotein gene. The DNA sequence containing ORF-1 was transiently expressed in COS-1 cells, and the viral protein produced in these cells was found to react with anti-MDV serotype-1 Antigen B-specific monoclonal antibodies. These studies indicate that the protein encoded by ORF-1 has antigenic properties resembling Antigen B of MDV-1. A gene homologous to ORF-1 was detected in the genome of both MDV-2(SB1) and MDV-3(HVT), which serve as commercial vaccine strains. Two additional ORFs were noted in the 4556 nucleotide sequence: ORF-2, which encodes a 333 aa polypeptide initiating in the UL and terminating in the TRL prior to the putative origin of replication, and ORF-3, which encodes a 155 aa polypeptide that is partly homologous to the phosphoprotein pp38 encoded by the BamHI-H sequence. The 65 N-terminal aa of the two gene products are identical, both being derived from the nucleotide sequences in the TRL and IRL, respectively. Additional homologous aa sequences are the hydrophobic aa domain in the middle of both proteins. The functions of ORF-2, ORF-3, and additional ORFs are under study.

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.

Herpes simplex virus type 1 long-term persistence, latency, and reactivation in infected Burkitt lymphoma cells

The two herpes simplex virus type 1 (HSV-1) strains F and AK which differ in virus-cell interaction and in DNA organization, were used to establish persistently productive infections in Burkitt lymphoma-derived cell lines BJAB and Raji. Four such lines could be maintained over a period of three years. Like the uninfected parental lines, the persistently infected cells display a cyclic pattern of cell proliferation. The expression of HSV-1-specific antigens proved to be variable. As a consequence, virus yields also vary within a subcultivation period. Pooled human HSV antisera, when continuously present, suppress virus production (inducible latency) and support cell proliferation to higher rates. By contrast, removal of the antiserum after a certain period of cultivation leads to virus reactivation with a delay of 8 to 20 days. After cultivation periods of more than 3 to 12 weeks, replacement of HSV antiserum does no longer result in virus reactivation and even inducers fail to reactivate.

Elimination of UL56 gene by insertion of LacZ cassette between nucleotide position 116030 to 121753 of the herpes simplex virus type 1 genome abrogates intraperitoneal pathogenicity in tree shrews and mice

In order to investigate whether or not the UL56 gene is involved in those processes determining the viral pathogenicity and latency, a recombinant virus HSV-1-M-LacZ was constructed in which the DNA sequences between nucleotide position (np) 116030 and 121753 were replaced by the E. coli beta-galactosidase (LacZ) gene. This deletion spans from the carboxyterminus of UL55 (np 116030) to the second exon of IE110 (np 121753) eliminating UL56 and the variable region of the BamHI DNA fragment B which were implicated in intraperitoneal pathogenicity and latency. The host range and growth kinetics of the recombinant virus HSV-1 M-LacZ were comparable to the parental strain HSV-1 F. As expected it was found that HSV-1-M-LacZ lost its virulent phenotype and was not able to develop acute infection in animals. The state of the UL56 gene was investigated by determining the cDNA sequence of the UL56 gene transcript of HSV-1 F using PCR products obtained after amplification of the cDNA with oligonucleotide primers corresponding to the translational start and stop codons of this gene. This analysis revealed that the DNA sequence of the UL56 gene of HSV-1 F differed from those DNA sequences determined for the genomic DNA of HSV-1 strain 17. Between nucleotide position 116343 and 116344 two nucleotides -AG- are inserted which prolong the ORF of the UL56 gene to 233 amino acids with a predicted molecular weight of 30 kDa.

In vitro transcription and translation of proteins encoded by the BamHI-B genomic fragment of herpes simplex virus-1

The BamHI-B DNA fragment of herpes simplex virus type-1 (HSV-1) is associated with intraperitoneal pathogenicity. Among the recently mapped RNA transcripts from this fragment (15), one was reported to be associated with latency. To relate the RNA transcripts to virus pathogenicity, the in vitro-transcribed RNAs from BamHI-B fragments of three HSV-1 strains--F (pathogenic), R19, and HFEM (apathogenic), were studied by in vitro translation. When the BamHI-HpaI (0.738-0.755 map units) DNA fragment from HSV-1 strain F was transcribed rightward and translated, three proteins of 70, 63, and 51 kD were detected. The 63 kD protein resembles in size and orientation the protein encoded by the ICP-27 (IE-2) gene (0.740-0.749 mu). The 51 kD polypeptide is assumed to be a prematurely terminated form of this protein. No proteins were obtained from RNA transcribed in the opposite direction. The SalI-NcoI (0.746-0.761 mu) fragment of the three HSV-1 strains yielded two proteins of 25 and approximately 15 kD when transcribed rightward and a 35 kD polypeptide from RNA transcribed in the opposite direction. As a result of the genomic deletion in HFEM, it was possible to obtain the 35 kD protein from the SalI-SalI DNA fragment (0.746-0.761 mu) as well. In vitro transcription and translation of the PstI-SalI (0.778-0.790 mu) DNA fragment (the right-hand side of HpaI-P) did not result in protein synthesis. The possibility that the UL56 gene is connected with the intraperitoneal pathogenicity of HSV-1 is discussed.

Identification and mapping of the UL56 gene transcript of herpes simplex virus type 1

The herpes simplex virus type 1 (HSV-1) strain HFEM is apathogenic for tree shrews and mice by the intraperitoneal application route. This is due to a 4.1 kbp deletion [0.762 to 0.789 map units (mu)] within the BamHI DNA fragment B of the viral genome. With exception of 71 bp the DNA sequences of the deleted region are located within the repetitive DNA sequences of the inverted repeat of the L segment of the HSV-1 genome (IRL). A 1.5 kb RNA hybridizing to the DNA sequences of the HSV-1 genome at map position 0.760-0.762 (BssHII DNA fragment F, part of the BamHI DNA fragment B) was found to be missing in cells infected with HSV-1 HFEM and other apathogenic HSV-1 strains. A detailed analysis of the transcriptional profile of this region of the pathogenic prototype strain HSV-1 F and strand-specific hybridizations revealed that this 1.5 kb RNA species is transcribed at 2 to 4 h p.i. in leftward orientation. The corresponding open reading frame in the HSV-1 genome had been predicted as the UL56 gene. The absence of this 1.5 kb RNA in HSV-1 HFEM-infected cells is due to the fact that the promoter region of the UL56 gene is located within those DNA sequences which are deleted in the HSV-1 HFEM genome. A specific DNA fragment (650 bp) was amplified by reverse polymerase chain reaction using oligonucleotide primers corresponding to the predicted translational start and termination region of the UL56 gene. The corresponding cDNA had been derived from cellular RNA from HSV-1 F-infected cells using oligo(dT) priming. This indicates that the 1.5 kb RNA is the real transcript of the UL56 gene of HSV-1.

The region 0.7615-0.796 m.u. of the HSV-1 genome determines suppression of humoral antibody formation against herpes simplex virus

The influence of genetic properties of parts of the HSV-1 genome on suppression of humoral antibody formation was investigated by using intratypic recombinants. The deleted strain HFEM (HSV-1) induces suppression. The MluI DNA fragment (coordinates 0.7615-0.796 m.u.) derived from the antibody inducing strain F1 (HSV-1) was transfected into the deleted strain HFEM to produce the recombinant virus R-M1CI and shown to restore antibody formation, as demonstrated by neutralization- and ELISA-tests. The intratypic recombinant viruses R-15, R-19 and R-26, produced by transfection of the Bam HI DNA-fragment B (0.738-0.809 m.u.) of strain F1 into the deleted strain HFEM, resulted in antibody formation only in the recombinant virus R-26. The reason for these different properties might be associated with the presence of small deletions in the SmaI A-fragment (0.763-0.765 m.u.) or elsewhere in the Bam HI DNA-fragment B. Our results were finally correlated to replication of the recombinant viruses in macrophages and to spread into spleen and adrenal glands. There is evidence that antibody formation may be correlated to the ability of HSV to replicate in macrophages.

Expression of human immunodeficiency virus type 1 gag gene using genetically engineered herpes simplex virus type 1 recombinants

Infectious herpes simplex virus type 1 (HSV-1) recombinants were constructed by inserting the cDNA sequence of the human immunodeficiency virus type 1 (HIV-1) gag gene (from nucleotide position 675 [SacI] to 3859 [Asp718] of the cDNA sequences of HIV-1 strain BH-10) within the DNA sequences of the BamHI DNA fragment B of the genome of an apathogenic HSV-1 strain HFEM. This HSV-1 strain possesses a 4.1-kbp deletion within the BamHI DNA fragment B between 0.762 and 0.789 map units of the viral genome, which allows the insertion of at least 4 kbp of foreign genetic material into this particular region. The DNA sequences of the immediate early promoter (IE4) of HSV-1 that were inserted upstream from the gag gene were used as a promoter. The screening of 205 virus stocks derived from individual plaques revealed that 46 recombinant viruses harbor HIV-1 gag-specific DNA sequences. However, it was found that only six of the recombinant viruses are able to express the gag gene product of HIV-1. This indicates that the ratio of the positive recombination events is about 2.9%.

Spatial and temporal distribution of bovine herpesvirus 1 transcripts

Northern (RNA) blot analysis was used to determine the spatial and temporal distribution of bovine herpesvirus 1 (BHV-1) transcripts. Total RNA was isolated from Madin-Darby bovine kidney cells which had been infected with BHV-1.2b strain K22 or BHV-1.1 strain Jura in the presence or absence of metabolic inhibitors. Cloned restriction fragments representing the entire genome of strain K22 were labeled with 32P and hybridized to immobilized RNA. A total of 54 BHV-1 transcripts were found, ranging in size from 0.4 to larger than 8 kilobases (kb). The inverted repeat regions and an adjacent segment of the unique large part of the BHV-1 genome encoded three major immediate-early (IE) transcripts and one minor IE transcript enriched after cycloheximide treatment of infected cells. Late transcripts were identified by drastically reduced abundance after cytosine arabinoside (araC) treatment. Twelve late transcripts were encoded mainly by the unique long genome region, with a cluster of four transcripts located on HindIII fragment K (map units 0.677 to 0.733). The 21 transcripts unaffected by araC treatment were defined as early; they showed dispersed locations over the whole genome, with a cluster on the unique short sequence. The 17 remaining transcripts could not be classified unambiguously as early or late by these techniques. The IE transcript with a size of 4.2 kb exhibited homology with the single IE gene of pseudorabies virus, and the IE transcript with a size of 2.9 kb was encoded in part by the genome region known to be transcriptionally active during latency.