The terminal repetition of herpes simplex virus DNA

Circularization and cleavage of guinea pig cytomegalovirus genomes

The mechanisms by which herpesvirus genome ends are fused to form circles after infection and are re-formed by cleavage from concatemeric DNA are unknown. We used the simple structure of guinea pig cytomegalovirus genomes, which have either one repeated DNA sequence at each end or one repeat at one end and no repeat at the other, to study these mechanisms. In circular DNA, two restriction fragments contained fused terminal sequences and had sizes consistent with the presence of single or double terminal repeats. This result implies a simple ligation of genomic ends and shows that circularization does not occur by annealing of single-stranded terminal repeats formed by exonuclease digestion. Cleavage to form the two genome types occurred at two sites, and homologies between these sites identified two potential cis elements that may be necessary for cleavage. One element coincided with the A-rich region of a pac2 sequence and had 9 of 11 bases identical between the two sites. The second element had six bases identical at both sites, in each case 7 bp from the termini. To confirm the presence of cis cleavage elements, a recombinant virus in which foreign sequences displaced the 6- and 11-bp elements 1 kb from the cleavage point was constructed. Cleavage at the disrupted site did not occur. In a second recombinant virus, restoration of 64 bases containing the 6- and 11-bp elements to the disrupted cleavage site restored cleavage. Therefore, cis cleavage elements exist within this 64-base region, and sequence conservation suggests that they are the 6- and 11-bp elements.

[Herpesviridae: classification and structure in 1991]

In 1981, herpesviruses were classified by the International Committee of Taxonomy of Viruses (ICTV, 1) inside the herpesviridae family. Progress in biotechnology and molecular biology during the last 10 yr, has permitted the characterization of new viruses and genomic structures. The objective of this paper is to collect the data found in the literature since 1981, to actualize the description of herpesviridae family.

Improved sensitivity of restriction endonuclease analysis of herpes simplex virus type 2 DNA with polyacrylamide gradient gel electrophoresis

Polyacrylamide gradient gel electrophoresis was used to resolve fragments of herpes simplex virus type 2 (HSV-2) DNA, produced by the restriction endonucleases Alu I, Bam HI, Pst I, and Sma I, which cleave the HSV-2 DNA into more than 30 fragments each. HSV-2 strains isolated from different individual patients could be easily distinguished from each other by the endonucleases Bam HI and Sma I. Successive virus isolates from a single person, analyzed using Alu I and Sma I, showed variability of fragment patterns. The effect of passaging the virus in cell cultures for several cycles was evaluated with the restriction endonuclease Alu I. No differences were found after 29 successive passages in VERO cells. Polyacrylamide gradient gel analysis of restriction endonuclease digests of HSV-2 DNA enables the use of enzymes that cleave the DNA into a great number of fragments, thus improving the sensitivity of analysis.

Structural organization of human herpesvirus DNA molecules

The herpesviruses are among the largest and most complex of all DNA viruses, and their genomes display an astonishing diversity in size, structure, and organization. In 1974, the features of large inverted repeats and structural isomerization were first discovered, and these proved to be characteristic properties of many herpesvirus genomes. Since then, research using the powerful techniques of modern molecular biology has revealed a great deal of comparative structural information about the arrangement of repetitive sequences and the location, structure, and primary nucleotide sequences of the genes for several easily assayed or abundantly expressed gene products. Extensive restriction enzyme cleavage maps and complete sets of cloned DNA fragments have been constructed for each of the five human herpesviruses, HSV-1, HSV-2, CMV, EBV, and VZV, and the entire 175,000-bp nucleotide sequence of EBV DNA has been determined. Based on these maps and reagents, the procedures of "DNA fingerprinting" and "dot hybridization" are proving useful at a clinical level for characterization of isolates and studying herpesvirus epidemiology. Strain differences, localized heterogeneity, tandem-repeat-defective genomes, and sites of cell-virus DNA homology have been described in some detail. The attention of basic researchers is now turning to equating structure with function, and rapid progress is expected in studies aimed at a better understanding of the mechanisms of viral DNA replication, maintenance of the latent state, reactivation, transformation, packaging, and regulation of the lytic cycle, etc using cloned functionally active DNA fragments, isolated intact genes and promoters, and DNA transfection and in vitro expression systems.

Structure and role of the herpes simplex virus DNA termini in inversion, circularization and generation of virion DNA

The herpes simplex virus genome consists of two components, L and S, which invert relative to each other during viral replication. The a sequence is present at the genomic termini in direct orientation and at the L-S junction in inverted orientation. Previously, we showed that insertion of a fragment spanning the L-S junction into the viral genome causes additional inversions. In this study, we determine the nucleotide sequence of the genomic termini and show that insertion of either the free S terminus or the L terminus causes inversions in the viral genome. We conclude that the a sequence is the inversion-specific sequence, that linear unit-length molecules packaged in virions are generated by cleavage between adjacent copies of the a sequence, that cleavage produces 3' single-base extensions on the genomic termini and that the signal for cleavage is contained within the a sequence.

Structure and expression of class II defective herpes simplex virus genomes encoding infected cell polypeptide number 8

Defective genomes present in serially passaged virus stocks derived from the tsLB2 mutant of herpes simplex virus type 1 were found to consist of repeat units in which sequences from the U(L) region, within map coordinates 0.356 and 0.429 of standard herpes simplex virus DNA, were covalently linked to sequences from the end of the S component. The major defective genome species consisted of repeat units which were 4.9 x 10(6) in molecular weight and contained a specific deletion within the U(L) segment. These tsLB2 defective genomes were stable through more than 35 sequential virus passages. The ratios of defective virus genomes to helper virus genomes present in different passages fluctuated in synchrony with the capacity of the passages to interfere with standard virus replication. Cells infected with passages enriched for defective genomes overproduced the infected cell polypeptide number 8, which had previously been mapped within the U(L) sequences present in the tsLB2 defective genomes. In contrast, the synthesis of most other infected cell polypeptides was delayed and reduced. The abundant synthesis of infected cell polypeptide number 8 followed the beta regulatory pattern, as evident from kinetic studies and from experiments in which cycloheximide, canavanine, and phosphonoacetate were used. However, in contrast to many beta (early) and gamma (late) viral polypeptides, the synthesis of infected cell polypeptide number 8 was only minimally reduced when cells infected with serially passaged tsLB2 were incubated at 39 degrees C. The tsLB2 mutation had previously been mapped within the domains of the gene encoding infected cell polypeptide number 4, the function of which was shown to be required for beta and gamma viral gene expression. It is thus possible that the tsLB2 mutation affects the synthesis of only a subset of the beta and gamma viral polypeptides. An additional polypeptide, 74.5 x 10(3) in molecular weight, was abundantly produced in cells infected with a number of tsLB2 passages. This polypeptide was most likely expressed from truncated gene templates within the most abundant, deleted repeats of tsLB2 defective virus DNA.

Site-specific cleavage/packaging of herpes simplex virus DNA and the selective maturation of nucleocapsids containing full-length viral DNA

Defective genomes present in serially passaged herpes simplex virus (HSV) stocks have been shown to consist of tandemly arranged repeat units containing limited sets of the standard virus DNA sequences. Invariably, the HSV defective genomes terminate with the right (S component) terminus of HSV DNA. Because the oligomeric forms can arise from a single repeat unit, it has been concluded that the defective genomes arise by a rolling circle mechanism of replication. We now report on our studies of defective genomes packaged in viral capsids accumulating in the nuclei and in mature virions (enveloped capsids) translocated into the cytoplasm of cells infected with serially passaged virus. These studies have revealed that, upon electrophoresis in agarose gels, the defective genomes prepared from cytoplasmic virions comigrated with nondefective standard virus DNA (M(r) 100 x 10(6)). In contrast, DNA prepared from capsids accumulating in nuclei consisted of both full-length defective virus DNA molecules and smaller DNA molecules of discrete sizes, ranging in M(r) from 5.5 to 100 x 10(6). These smaller DNA species were shown to consist of different integral numbers (from 1 to approximately 18) of defective genome repeat units and to terminate with sequences corresponding to the right terminal sequences of HSV DNA. We conclude on the basis of these studies that (i) sequences from the right end of standard virus DNA contain a recognition signal for the cleavage and packaging of concatemeric viral DNA, (ii) the sequence-specific cleavage is either a prerequisite for or occurs during the entry of viral DNA into capsid structures, and (iii) DNA molecules significantly shorter than full-length standard viral DNA can become encapsidated within nuclear capsids provided they contain the cleavage/packaging signal. However, capsids containing DNA molecules significantly shorter than standard virus DNA are not translocated into the cytoplasm.

The genome of frog virus 3, an animal DNA virus, is circularly permuted and terminally redundant

We examined the structure of the frog virus 3 (FV 3) genome by using electron microscopic and biochemical techniques. The linear FV 3 DNA molecules (Mr approximately 100 x 10(6) formed circles when partially degraded with bacteriophage lambda 5'-exonuclease and annealed, but not when the annealing was done without prior exonuclease digestion. The results suggest that the DNA molecules contain direct terminal repeats. The repeated region composed about 4% of the genome. Complete denaturation of native FV 3 DNA molecules followed by renaturation produced duplex circles each bearing two single-stranded tails at different points along the circumference. The tails presumably represent the terminal repeats. The formation of duplex circles suggests that the FV 3 genome is circularly permuted. This is further borne out by (i) failure to identify a specific restriction endonuclease fragment containing the label when the molecular ends were radiolabeled by using the polynucleotide kinase procedure, and (ii) similarity in the restriction patterns of virion DNA and large concatemeric replicating viral DNA as revealed by endonucleolytic cleavage of both DNAs with HindIII. From the above data, we conclude that the FV3 genome is both circularly permuted and terminally redundant--unique features for an animal virus.

Localization of an origin of DNA replication within the TRS/IRS repeated region of the herpes simplex virus type 1 genome

An assay has been developed and used to locate an origin of DNA replication on the herpes simplex virus type 1 (HSV-1) genome. Baby hamster kidney cells were transfected with circular plasmid molecules containing cloned copies of HSV-1 DNA fragments, and helper functions were provided by superinfection with wild-type HSV-1. The presence of an HSV-1 origin of replication within a plasmid enabled amplification of the vector DNA sequences, which was detected by the incorporation of [32P]orthophosphate. By screening various HSV-1 DNA fragments it was possible to identify a 995-bp fragment that maps entirely within the reiterated sequences flanking the short unique region of the viral genome and contains all the cis-acting signals necessary to function as an origin of viral DNA replication. The products of plasmid replication were shown to be high mol. wt. DNA molecules consisting of tandem duplications of the complete plasmid, suggesting that replication was occurring by a rolling-circle mechanism.

Characterization of coliphage lambda hybrids carrying DNA fragments from Herpes simplex virus type 1 defective interfering particles

We describe the characterization of 34 hybrid lambda bacteriophages carrying EcoRI fragments obtained from DNA of defective interfering particles of the Patton strain of Herpes simplex virus type 1 (HSV-1). All cloned fragments contained S region terminal repeat sequences (TRs) fused to unique HSV-1 DNA. Several fragments contained deletions and rearrangements not described previously for DNA of HSV-1 defective interfering particles. A model describing the generation of defective interfering DNA based on recombination events involving the terminal "a" sequence as presented.

Structure of replicating herpes simplex virus DNA

We have investigated the molecular anatomy of the herpes simplex virus replicative intermediates by cleavage with the restriction endonuclease BglII. We find that in populations of multiply infected cells, pulse-labeled replicating herpes simplex virus DNA contains at least two and probably all four sequence isomers. Also, it contains no detectable termini. In pulse-chase experiments, we show that endless replicative intermediates are the precursors to virion DNA and that maturation is a relatively slow process. The results are discussed in terms of their significance to possible models of herpes simplex virus DNA replication.

Method for induction of mutations in physically defined regions of the herpes simplex virus genome

A procedure was developed for inducing mutations in isolated restriction enzyme fragments of herpes simplex virus type 1 (HSV-1) DNA with nitrous acid. The mutations were then transferred to the viral genome by genetic recombination during cotransfection of rabbit kidney cells with the mutagenized fragments and intact HSV-1 DNA. The HpaI restriction enzyme fragments LD, B, LG, I, and J were mutagenized. Temperature-sensitive mutants were found at frequencies of 1 to 5% among the progeny of the transfections. Syncytial mutants also were found at high frequency when fragment B or LD was used for mutagenesis. Fifteen of these mutants, 11 temperature sensitive and 4 syncytial, were used for further studies, including complementation analysis, DNA synthesis, and marker rescue. Marker rescue data presented here and in the accompanying publication (A. L. Goldin, R. M. Sandri-Goldin, M. Levine, and J. C. Glorioso, J. Virol. 38: 50-58, 1981) confirm the map position of some of the newly isolated mutants.

Cloning of herpes simplex virus type 1 sequences representing the whole genome

Sequences representative of the whole genome of herpes simplex virus type 1 (HSV-1) strain KOS were cloned in the plasmid vector pBR325 in the form of EcoRI-generated DNA fragments. The cloned fragments were identified by digestion of the chimeric plasmid DNA with restriction enzymes EcoRI or EcoRI and BglII followed by comparison of their electrophoretic mobilities in agarose gels with that of similarly digested HSV-1 virion DNA. The cloned fragments showed the same migration patterns as the corresponding fragments from restricted virion DNA, indicating that no major insertions or deletions were present. The presence of HSV-1 sequences in the chimeric plasmids was confirmed by hybridization of plasmid DNA to HSV-1 virion DNA. Additionally, some of the cloned fragments were shown to be biologicaly active in that they efficiently rescued three HSV-1 temperature-sensitive mutants in cotransfection marker rescue experiments.

Isolation and translation of mRNA encoded by a specific region of the herpes simplex virus type 1 genome

We have examined in detail the major mRNA species encoded by the region of the herpes simplex virus type 1 genome encoded by HindIII fragment K (0.53-0.59 from the left end of the prototype arrangement of the genome) by using this restriction fragment bound to cellulose as a reagent for isolation of this mRNA. Before viral DNA replication in infected cells (early), a major species of viral mRNA 5.2 kilobases (kb) in length is abundant. After the onset of viral DNA replication (late), four mRNA species are abundant: 7, 5.2, 3.8, and 1.8 kb in size. We have used reverse transcriptase from avian myeloblastosis virus to make DNA complementary to these RNA species and their 3' ends. We have shown by hybridization of this complementary DNA to Southern blots of herpes simplex virus type 1 DNA that the 7-, 5.2-, and 1.8-kb mRNA species have their 3' ends to the right of 0.59 and are at least partially colinear. The 3.8-kb mRNA has a 3' end mapping to the left of the 3' ends of these other species. In vitro translation of HindIII fragment K-specific mRNA in a reticulocyte lysate system yielded three major polypeptide products: 140,000, 122,000, and 54,000 daltons (d). Less prominent species of 86,000 and 65,000 d also were produced. Translation of size-fractionated HindIII fragment K-specific mRNA showed that the 7-, 5.2-, and 3.8-kb mRNA's encoded the 54,000-, 140,000-, and 122,000-d polypeptides, respectively. The 140,000-d polypeptide was the major polypeptide translated using early HindIII fragment K-specific mRNA as a template. The 3.8-kb mRNA also encoded the 86,000-d polypeptide, whereas the 1.8-kb mRNA encoded a polypeptide that was indistinguishable from the 54,000-d polypeptide encoded by the 7-kb mRNA, in addition to the 65,000-d polypeptide. The implications of the data are discussed.

Cloning of herpes simplex type 1 DNA fragments in a bacteriophage lambda vector

DNA isolated from defective and nondefective virions of herpes simplex type 1 (HSV-1) (strain Patton) was digested with restriction endonucleases, and the resulting DNA fragments were inserted in the EK2 coliphage vector lambdagtWES . lambdaB. The recombinant DNA was encapsidated in vitro under P4 maximum containment conditions. These lambda-HSV1 hybrids were purified and amplified, and the DNA was isolated in the P4 facility. DNA, free of viable phage and bacteria, was removed from P4 conditions and analyzed. Represented among the hybrids studied to date are DNA fragments from about 50 percent of the normal HSV-1 genome. The hybrids derived from defective HSV-1 DNA fragments demonstrate the existence of many similar but not identical classes of defective genomes.

Rolling hairpin model for replication of parvovirus and linear chromosomal DNA

A novel, quasicircular scheme is proposed for the replication of parvovirus DNA. Daughter strands are initiated after the copying and rearrangement of a terminal palindromic sequence, a process termed 'hairpin transfer'. Such a process may be involved in the replication of other viruses and host cell DNA.

Variation in the molecular size of the DNA from closely related strains of type I herpes simplex virus

We have investigated the comparative genome size of five strains of HSV type 1 (HSV-1). Two of these strains have a common origin and differ in their plaque morphology on HeLa cells, one strain is a wild type isolate, and two others are established laboratory strains. All strains show high sequence homology based on the melting behavior of heteroduplexes. The greatest sequence divergence between any two strains was found to be no more than 10%. There are real differences in the size of the genomes of these strains of HSV-1 as measured by electron microscopy. The shortest and largest genomes measured differ in size by 10%, however, the size of the genomes of all strains are within 5% of a median valve of 87-88X106.