Neil M. Wilkie

Nucleotide sequences of the joint between the L and S segments of herpes simplex virus types 1 and 2.

The a sequence of herpes simplex virus (HSV) is present as a direct repeat at the genomic termini and also in inverted orientation at the joint between the L and S segments. DNA sequences have been determined for the joint regions of the genomes of HSV-1 and HSV-2, and relative to these sequences the genomic termini are in both cases located close to a short direct repeat of 17 to 21 base pairs (bp) at the b-a and a-c junctions. The HSV-1 joint region contains three separate tandem direct reiterations of short sequences, (12, 16 and 17 bp in strain 17) and we conclude that size heterogeneity in the a and c sequences is due to variable copy numbers of these repeated units. It is likely that a considerable part of the HSV-1 joint region does not code for polypeptide.

Temporal regulation of herpes simplex virus type 1 transcription: location of transcripts on the viral genome

Abstract Nuclear and cytoplasmic viral RNAs, synthesized in cells productively infected with herpes simplex virus type 1 at early and late times post-infection and in the presence of DNA and protein synthesis inhibitors, have been analyzed by blot hybridization to viral DNA fragments generated by single and double digests with the Hind III, Bgl II and Hpa I restriction endonucleases. RNA transcribed in the presence of cycloheximide (immediate early, made using a cell RNA polymerase) hybridizes to restricted portions of the HSV-1 genome, and the hybridization patterns of both nuclear and cytoplasmic immediate early RNAs are similar. This finding suggests that synthesis of immediate early RNA within the nucleus may be restricted; alternatively, there may be rapid processing of primary transcripts. Virus-induced protein synthesis is a prerequisite for the switch from the restricted immediate early to the early pattern of transcription in which there is hybridization to all the DNA fragments. The hybridization pattern of RNA labeled in the presence of cytosine arabinoside resembles that of early RNA. Late RNA also hybridizes to all the DNA fragments, but the relative hybridization to the individual DNA fragments is different between early and late times. When late nuclear and late cytoplasmic RNAs are compared, there is greater relative hybridization to several different regions of the genome with nuclear RNA. This implies that either translocation of transcripts to the cytoplasm is regulated or that certain RNAs are degraded more rapidly within the cytoplasm.

The Synthesis and Substructure of Herpesvirus DNA: the Distribution of Alkali-labile Single Strand Interruptions in HSV-1 DNA

Summary Denatured DNA of herpes simplex virus was released from the particles using an alkaline detergent, Decon-75. The largest single strands sedimented on alkaline sucrose gradients with a mol. wt. of 47.2 ± 0.33 × 106, slightly less than half the value calculated for the intact duplex (104 × 106). About 50% of the DNA was found in fragments which sedimented slower than this in a heterogeneous manner. On agarose gel electrophoresis the largest strands migrated with a mol. wt. of 40 × 106. The reason for this difference is not known but since the individual strands of T 4 DNA were shown to migrate with slightly different Rr values, factors other than mol. wt. may affect the migration of single-stranded DNA. Two fragments of mol. wt. 35 × 106 and 30 × 106 were observed but the rest of the fragments remained unresolved by this technique. Virus DNA associated with the nucleus of infected cells had a much lower mol. wt. than particle DNA (3.2 × 106). Although this value increased if the DNA was isolated from intact cells, the average sedimentation coefficient of nuclear virus DNA was never as high as the largest strands of particle DNA. When the largest single strands from particles were prepared by sucrose gradient fractionation they exhibited a unimodal mol. wt. distribution after both sedimentation and electrophoretic analysis. These ‘intact’ single strands were annealed and analysed by banding in CsCl gradients and by analyses employing the Neurospora crassa endonuclease. The results show that the ‘intact’ strands reassociated with the same kinetics and to the same extent as total virus DNA, suggesting that both strands of the duplex were present in equal amounts.

Location and Orientation of Homologous Sequences in the Genomes of Five Herpesviruses

Molecular hybridization experiments were carried out to investigate homologous regions in the genomes of herpes simplex virus types 1 and 2 (HSV-1 and HSV-2), equid herpesvirus 1 (EHV-1), pseudorabies virus (PRV) and varicella-zoster virus (VZV). Virion DNA probes from EHV-1, PRV and VZV hybridized to similar regions of the HSV genome, and the use of cloned DNA probes allowed heterologous genomes to be oriented with respect to homologous regions. The HSV-1 and HSV-2 genomes are colinear, the EHV-1 and VZV genomes are colinear with the IL or ISL genome arrangement of HSV, and the PRV genome is essentially colinear with the IL genome arrangement of HSV except that the region 0.1 to 0.4 fractional genome units appears to be inverted. A detailed analysis of sequences in the HSV-2 and PRV genomes to which the HSV-1 major capsid protein gene hybridized was carried out in order to demonstrate the application of molecular hybridization to the location of genes in heterologous genomes. The lesion in a DNA-positive temperature-sensitive mutant of PRV was mapped within the putative PRV major capsid protein gene. We conclude that the herpesviruses we have studied possess several highly conserved genes, and propose that they are similar in genetic organization despite presumably separate evolutionary histories.

Physical and genetic analysis of the herpes simplex virus DNA polymerase locus

Abstract The physical location of the mutations ts C7, ts C4, and ts D9 (strain KOS), all of which affect HSV DNA polymerase, have been located on the physical map of the HSV-1 genome. Intertypic recombinants between HSV-1 mutants ts C4, ts D9, and ts C7 and HSV-2 (strain HG52) were generated by marker rescue. Restriction endonuclease analysis using five restriction enzymes led to the identification of the parental origin of the DNA sequences in the genomes of 15 recombinants of HSV-1 ts D9 with HSV-2, 13 recombinants of HSV-1 ts C7 with HSV-2, and 12 recombinants of HSV-1 ts C4 with HSV-2. In addition to the ts marker used for selection, a nonselected marker (phosphonoacetic acid resistance, paa r ) was present in all the crosses. All the mutations cluster in a 4.9-kilobase pair (kbp) region between map units 38.6 to 41.8. The mutations for paa r and ts D9 map within a 2.9-kbp region (40 to 41.8 map units). The ts C7 mutation is contained in a 1.5-kbp region to the left of the other (map units 38.6 to 39.6). The mapping limits for the mutation ts C4 are between map units 39.3 and 41.8. The mutations, at this point, have not been assigned to specific genes but the physical mapping results presented in this study clearly show clustering of these mutations in a discrete region of the genome.

Resistance of herpes simplex virus to acycloguanosine—genetic and physical analysis

Abstract Resistance of herpes simplex viruses (HSV-1 and HSV-2) to acycloguanosine (ACG) is determined by the two genetic loci of HSV coding for deoxypyrimidine kinase (thymidine kinase) and DNA polymerase activity. Mutants of HSV-1 which induce defective deoxypyrimidine kinase (dPyK − mutants) activity can participate in interallelic complementation, and show variability in their resistance to acycloguanosine (ACG R ). This allows for subdivision of dPyK − mutants based on their resistance to ACG. Mutants dPyK − and dPyK −11 are in one interallelic complementation group and both are 100-fold more resistant to ACG in a plaque reduction assay than is wild type herpes simplex virus type 1 (HSV-1). (The 50% inhibitory concentrations (ID 50 ) are 6.0 and 7.0 μM of ACG compared to 0.06 μM .) Mutant MDK (Kit) which cannot complement any other mutant is 500-fold more resistant to ACG (ID 50 = 50 μM ). Other dPyK − mutants fall in between in their sensitivity to ACG. The map position of the mutations in the DNA polymerase locus which result in resistance to ACG ( acg r ) was located by correlating the ACG sensitivity of HSV-1IHSV-2 intertypic combinants with restriction endonuclease analysis of their DNA. The mutations acg r and paa r (phosphonoacetic acid resistance) are contained in the same 1.3 kbp region of DNA (map units 40.2 to 41.0). The level of sensitivity to ACG is type specific, differing in HSV-1 and HSV-2. This type specificity is determined by DNA sequences within map units 39.6 to 41.0. Thus the DNA sequences for type-specific sensitivity and resistance to ACG are shown to be distinct and clustered in the same region as the HSV DNA polymerase locus.

Analysis of Herpesvirus DNA Substructure by means of Restriction Endonucleases

The mol. wt. and molar ratios of the Hind III and Hpa I fragments of HSV-1 DNA and the Eco RI fragments of HSV-2 DNA have been determined. Results obtained suggest that DNA isolated from both HSV-1 and HSV-2 consists of molecules with four different sequence arrangements which are present in similar amounts. Our explanation of the cleavage patterns of these four genome arrangements with the different restriction enzymes is presented. Some of the possible implications of these four genome arrangements for genetic recombination are discussed.

Physical maps for HSV type 2 DNA with five restriction endonucleases.

The ordering of restriction endonuclease fragments of HSV-2 DNA for physical maps has been studied using molecular hybridization techniques and the cleavage of isolated restriction endonuclease fragments with further restriction endonucleases. Physical maps for the fragments produced by EcoRI, Hind III, Bgl II, Xba and Hpa I have been constructed. The mol. wt. of the various regions which constitute HSV-2 genome are very similar to the corresponding mol. wt. in the HSV-1 genome.

Inversion of the two segments of the herpes simplex virus genome in intertypic recombinants.

We have analysed by restriction site mapping the structures of the termini and L-S joint in several HSV-1/HSV-2 intertypic recombinants, including Bx1(28-1), the virion DNA of which has a marked overabundance of one orientation of the L segment, and subclones of Bx1(28-1). All recombinants with both orientations of L present in equal amounts contain TRL and IRL regions derived at least in part from the same parent (HSV-1 or HSV-2) as a result of previously undetected crossovers in these regions. Recombinants with a predominance of one orientation of L have TRL and IRL regions derived from different parents. Homology between a sequences alone at the L terminus and L-S joint is sufficient for normal inversion of L. Analysis of another recombinant, RE4, which fails to invert normally in both L and S, suggests that normal inversion of S is dependent upon the presence of TRS and IRS regions derived at least in part from the same parent. We conclude that segment inversion specifically depends upon the a sequence, that the process of DNA replication and maturation does not necessarily produce molecules with identical a sequences, and that direct ligation of termini may occur during DNA replication.

Physical mapping of temperature-sensitive mutations of herpes simplex virus type 1 by intertypic marker rescue

Abstract Ts + recombinant viruses were isolated from cells mixedly infected, at the nonpermissive temperature, with the intact DNA of HSV-1 ts mutants and unseparated fragments of wildtype HSV-2 DNA. Restriction enzyme analysis of the genomes of these intertypic recombinants enabled the cross-over points to be mapped. Recombinants generated with a particular ts mutant DNA contained relatively small overlapping insertions of HSV-2 DNA which enabled accurate physical mapping of the original ts lesion. Five ts mutations were mapped using this approach, and in each case, the results confirmed those previously obtained by marker rescue with isolated restriction endonuclease fragments of wild-type HSV-1 DNA.