Detection of pseudorabies virus transcripts in trigeminal ganglia of latently infected swine

Complete nucleotide sequence of the Marek's disease virus ICP4 gene

The Marek's disease virus (MDV) gene encoding a homologue to the ICP4 protein of herpes simplex virus has been mapped to BamHl fragment A based on the physical map of the MDV genome (Fukuchi et al., 1984). The gene lies completely within the inverted repeat flanking the unique short region of the genome. The complete nucleotide sequence of the MDV ICP4 gene has been determined. The coding region is 4245 nucleotides long and has an overall G+C content of 52%. The MDV ICP4 protein is predicted to have a structure similar to that of ICP4-like proteins of other herpesviruses in that it has five distinct regions, the second and fourth of which are highly conserved. In addition, the protein contains the characteristic run of serine residues located toward its amino terminus. The MDV ICP4 gene is expressed in MDV-infected chicken embryo fibroblasts.

Molecular basis of latency in pathogenic human viruses

Several human viruses are able to latently infect specific target cell populations in vivo. Analysis of the replication cycles of herpes simplex virus, Epstein-Barr virus, and human immunodeficiency virus suggests that the latent infections established by these human pathogens primarily result from a lack of host factors critical for the expression of viral early gene products. The subsequent activation of specific cellular transcription factors in response to extracellular stimuli can induce the expression of these viral regulatory proteins and lead to a burst of lytic viral replication. Latency in these eukaryotic viruses therefore contrasts with latency in bacteriophage, which is maintained primarily by the expression of virally encoded repressors of lytic replication.

Cloning of the latency gene and the early protein 0 gene of pseudorabies virus

A collection of overlapping cDNA clones encoding the latency transcript of pseudorabies virus and the DNA nucleotide sequence of the latency gene has been obtained. The transcript is spliced with 4.6 kb of intervening sequences. This mRNA, designated the large latency transcript, is 8.5 kb. It is polyadenylated and contains a large open reading frame capable of coding for a 200-kDa polypeptide. The direction of transcription is antiparallel to that of the immediate-early gene IE180 and a newly identified early gene, EP0. The latency transcript overlaps the entire IE180 gene and most of the EP0 gene. The EP0 mRNA is 1.75 kb and polyadenylated. The deduced amino acid sequence revealed the presence of cysteine-rich zinc finger domain similar to that of the immediate-early gene ICP0 of herpes simplex virus type 1 and the gene 61 polypeptide of varicella-zoster virus. On the basis of the biological functions, conserved protein domains, and unique spatial arrangements of the homologous polypeptides (IE180 versus ICP4 and EP0 versus ICP0) between pseudorabies virus and herpes simplex virus type 1, it is predicted that a homologous protein domain is also encoded by the 8.5-kb large latency transcripts of these two viruses.

Enzymatic amplification of latent pseudorabies virus nucleic acid sequences

To investigate various aspects of the latency of pseudorabies virus in swine (PRV, suid herpesvirus 1) we developed in vitro nucleic acid amplification methods based upon the polymerase chain reaction. Primers flanking a 156-bp region of the pseudorabies virus gp II gene were annealed to purified PRV DNA as well as DNA isolated from the trigeminal ganglia of swine latently infected with PRV and subjected to PCR amplification. Following amplification, 100 fg of PRV DNA was visualizable on stained gels and 1 fg (equivalent to 6 viral genome copies) was detectable when amplification was combined with blot hybridization. PRV-specific DNA sequences which remained undetectable by direct blot hybridization assays were amplified to levels visualizable on ethidium-bromide-stained gels in 5 of 5 experimental latently infected animals. In addition, oligonucleotide primers specific for a 223-bp region of the PRV immediate-early gene (IE 180) were capable of amplifying overlapping latency associated transcripts (LATs), via a cDNA intermediate, in 6 of 6 latently infected swine. These nucleic acid amplification methods should be applicable to the investigation of PRV latency, and gene expression during latency and reactivation, in which few cells harbor latent virus.

The 5' and 3' limits of transcription in the pseudorabies virus latency associated transcription unit

While latent in sensory neurons of infected pigs, pseudorabies virus expresses transcripts from a limited genomic area. These RNAs are transcribed from the strand opposite to that which encodes the pseudorabies immediate-early protein. Using a combination of in situ nucleic acid hybridization performed on latently infected pig trigeminal ganglia and DNA sequencing, 5' and 3' limits of transcription for the pseudorabies LAT transcription unit have been defined. The 5' limit of transcription has been localized to a NarI-BamHI subfragment of the BamHI-6 fragment. Several promoter elements in the correct orientation for the transcript are present including consensus TATA and CAAT boxes and an SP1 site. The 3' limit of transcription has been localized to a HindIII-KpnI subfragment of the BamHI-5 fragment which contains a consensus polyadenylation signal and two termination codones in the correct orientation. From these results we conclude that the region of pseudorabies virus DNA which is active during latency can be no longer than 12.6 kb and completely overlaps the gene encoding the pseudorabies immediate-early protein.

Characterization of the latency-related transcriptionally active region of the bovine herpesvirus 1 genome

Approximate 5' and 3' ends of the bovine herpesvirus 1 (BHV-1) latency-related RNA (LR RNA) were mapped in rabbit trigeminal ganglia (TG) by in situ hybridization. The data provide a size estimate of 0.77 to 1.16 kb for the LR RNA. An LR RNA mapping to a similar location was also detected in TG of cattle latently infected with BHV-1. The BHV-1 LR region is transcriptionally active in bovine cell cultures lytically infected with BHV-1. A 1.15-kb transcript, present at early and late times postinfection, of the same sense and approximate size that seen in latently infected TG overlaps a 2.9-kb immediate-early and a 2.6-kb early and late transcription unit present on the complementary strand. Sequence analysis of the LR RNA sense strand indicates the presence of a potential polymerase II promoter in close proximity to the 5' terminus of the LR RNA and two open reading frames within its map positions. The complementary strand contains the 3' portion of a large open reading frame that almost completely overlaps the map position of the LR RNA present on the opposite strand.

Pseudorabies virus immediate-early gene overlaps with an oppositely oriented open reading frame: characterization of their promoter and enhancer regions

The immediate-early (IE) gene of pseudorabies virus (PRV) has recently been sequenced for two virus strains. To investigate IE gene regulation and to examine the genome segment reported to encode latency-related transcripts in opposite polarity to the IE gene, sequence analysis has been extended by 5 kb from each end of the IE gene. The IE promoter (P1) was found to be more complex than previously recognized: it consisted of nine imperfect repeats, each containing five to six different consensus elements for transcription factor binding. A second promoter (P2) was discovered downstream of the IE gene. It contained numerous octamer consensus sequences (ATGCAAAT) and recognition sites for transcription factor Sp1; specific binding of nuclear proteins to four Sp1 sites was detected. An open reading frame (ORF3) bordering on P2 was identified, oriented antiparallel to the IE gene. Potential enhancer elements (E3 and E4) were isolated by the enhancer trap technique. Linked to P1 and a CAT indicator gene, E3 acted as an enhancer and E4 as a silencer. The PRV IE gene product repressed transcription from its own promoter and activated the SV40 early promoter. The transactivating virion protein Vmw65 of HSV1 had an opposite effect on these promoters.

Characterization of herpes simplex virus type 2 transcription during latent infection of mouse trigeminal ganglia

Using a cornea trigeminal ganglion model, we have investigated transcription by herpes simplex virus type 2 (HSV-2) during latency in mice. Latency was verified 2 months postinoculation by reactivation of HSV-2 after explant cocultivation of trigeminal ganglia from the majority of mice (83%). Transcription during latent HSV-2 infection was limited to the repeat regions of the viral genome as determined by in situ hybridization using restriction fragment probes representing 100% of the HSV-2 genome. Further mapping of the positively hybridizing region by using subfragments showed that transcription occurred from approximately 11.5 kb of contiguous DNA fragments. A 1.0-kb PvuI-BamHI fragment within the BamHI F fragment and a 0.3-kb BamHI-SalI fragment and a 3.4-kb SalI-BamHI fragment within the BamHI P fragment hybridized more strongly than other subfragments in in situ hybridization experiments. All positive signals were confined to the nucleus. The RNA that hybridized to the 3.4-kb SalI-BamHI DNA fragment probe by in situ hybridization corresponded to a 2.3-kb transcript on Northern (RNA) blots. Under our conditions for Northern blot hybridization, the 3.4-kb SalI-BamHI probe of HSV-2 hybridized to a limited degree with the latency-associated transcripts of HSV-1. Shorter spliced species of latency-associated transcript RNA, which are seen during HSV-1 latency, have not been detected in latent HSV-2 RNA. However, viral gene expression during HSV-2 latency appears to be very similar to that during HSV-1 latency.

A major portion of the latent pseudorabies virus genome is transcribed in trigeminal ganglia of pigs

Pseudorabies virus (PRV) is a porcine herpesvirus that establishes latent infections in trigeminal ganglia. To determine whether PRV expresses any transcripts that could play a role in latency, the trigeminal ganglia of 14 pigs previously inoculated through the nose and latently infected with PRV(Ka) were assayed by in situ nucleic acid hybridization for the presence of PRV-specific RNA. Hybridizations employing probes encompassing the entire viral genome revealed that an area extending from 0.64 to 0.82 map units was transcriptionally active. The DNA probe that most consistently detected transcripts was BamHI-8, a fragment which contains the gene for the immediate-early protein. With this probe, ganglia from 10 (71%) of 14 pigs scored positive for PRV RNA, although only 1 (8%) of 12 of the ganglia from the opposite side reactivated virus after explanation and culture of latently infected trigeminal ganglia. The RNA was transcribed from the strand opposite to that coding for the immediate-early protein; the signal was neuronally localized, with dense nuclear accumulation accompanied by variable numbers of grains over the cytoplasm. Northern RNA blot analysis showed that a discrete set of poly(A)- PRV transcripts were present in latently infected trigeminal ganglia. Additional in situ nucleic acid hybridization analysis revealed that the 3' limit of the transcriptionally active area was located in a 1.2-kilobase fragment upstream and adjacent to the 5' end of the immediate-early protein RNA, whereas the 5' limit was as much as 4.9 kilobases downstream from the 3' end of this RNA. PRV therefore expresses latent-phase transcripts that, although similar in many respects to latent-phase transcripts reported for other herpesviruses, have some unique properties.

Genetic basis for the pathogenesis of transmissible gastroenteritis virus

Intracellular RNAs of an avirulent small-plaque (SP) transmissible gastroenteritis virus variant and the parent virulent Miller strain of transmissible gastroenteritis virus were compared. Northern RNA blotting showed that the Miller strain contained eight intracellular RNA species. RNAs 1, 2(S), 5, 6(M), 7(N), and 8 were similar in size for both viruses; however, the SP variant lacked subgenomic RNAs 3 and 4. Instead, the SP virus contained an altered RNA species (delta 4) that was slightly smaller than RNA 4. S1 nuclease protection experiments showed a deletion of approximately 450 nucleotides in the SP genome downstream of the peplomer S gene. Sequencing of cDNA clones confirmed that SP virus contained a 462-nucleotide deletion, eliminating the transcriptional recognition sequences for both RNAs 3 and 4. These RNAs encode open reading frames A and B, respectively. An alternative consensus recognition sequence was not readily apparent for the delta 4 RNA species of SP virus. Since open reading frame A is missing in SP virus, it is not essential for a productive infection. The status of the potential protein encoded by open reading frame B is not clear, because it may be missing or just truncated. Nevertheless, these genes appear to be the contributing entities for transmissible gastroenteritis virus virulence, SP morphology, tissue tropism, and/or persistence in swine leukocytes.

Multiple bandshift assay: rapid identification and cloning of DNA fragments containing specific protein-binding sites

A new rapid method for the identification and cloning of DNA fragments containing specific protein-binding domains is based on the common bandshift assay. Cloned DNA is digested with a restriction endonuclease recognizing a particular 4-bp sequence, an aliquot of this digest is end-labelled and used in protein binding reactions with and without protein extract. The binding reactions are then loaded onto nondenaturing polyacrylamide gel. The main portion of the digest is run in a parallel lane and serves as a source of fragments for cloning. Autoradiography of the wet gel reveals loss in intensity of some bands from the restriction digest incubated with the protein extract. DNA fragments corresponding to these bands are cut out from the gel; DNA is eluted and cloned in the M13 vector, thus allowing rapid and simple sequencing of the inserts. The method, termed multiple bandshift assay, is especially useful when screening relatively long DNA fragments (of several kb) for potential protein-binding domains. The procedure was used to study interaction of HeLa-cell nuclear proteins with a 5.2-kb downstream region of pseudorabies virus immediate-early gene (C. Vlcek, Z. Kozmík, V. Paces, S. Schirm and M. Schwyzer, unpublished).

Pseudorabies virus latency: restricted transcription

Cloned pseudorabies virus (PRV) sequences representing over 80% of the viral genome were radiolabeled and individually hybridized to nucleic acid in the trigeminal ganglia of acutely and latently infected swine. In acutely infected animals, all cloned probes hybridized to PRV RNA and DNA. In contrast, during latency transcription was found to be limited to a selected region, corresponding to the IE gene, analogous to that of two other alpha-herpesviruses. Viral DNA was not detected in latently infected neurons by in situ hybridization.

The BamHI J fragment (0.706 to 0.737 map units) of pseudorabies virus is transcriptionally active during viral replication

The BamHI J fragment of the pseudorabies virus (PRV) genome has not been associated with any viral transcripts during viral replication. In this report, data are presented to show that a portion of BamHI-J is transcribed during a productive infection. Four oligo(dT)-cellulose-selected RNA species were detected by hybridization with probes derived from BamHI-J. These RNAs were partially colinear, and they were transcribed in the opposite orientation with respect to the immediate-early gene (IE180) of PRV. At least one of the transcripts overlapped (antisense) the coding sequence of IE180 by 450 nucleotides. Expression of these RNAs was sensitive to phosphonoacetic acid, indicating that they are transcripts of PRV late genes. There were several similarities between these RNAs and the latency-associated transcripts detected in the trigeminal ganglia of swine latently infected with PRV (A. K. Cheung, J. Virol. 63: 2908-2913, 1989).