Conformational changes induced in herpes simplex virus DNA polymerase upon DNA binding.

Herpesvirus DNA polymerases are prototypes for alpha-like DNA polymerases and important targets for antiherpesvirus drugs. We have investigated changes in the catalytic subunit of herpes simplex virus DNA polymerase following DNA binding by using the techniques of endogeneous fluorescence quenching and limited proteolysis. The fluorescence studies revealed a reduction in the rate of quenching by acrylamide in the presence of DNA without changes in the wavelength of the emission peak or in the lifetime of the fluorophore, consistent with the possibility of conformational changes. Strikingly, the proteolysis studies revealed that binding to a variety of natural and synthetic DNA and RNA molecules induced the appearance of a new cleavage site for trypsin near residue 1060 of the protein and increased cleavage by trypsin near the center of the protein. The extent of these cleavages correlated with the affinity of the polymerase for these ligands. These data provide strong evidence that binding to nucleic acid polymers induces substantial localized conformational changes in the polymerase. The locations of enhanced tryptic cleavage near sites implicated in substrate recognition and interaction with a processivity factor suggest that the conformational changes are important for catalysis and processivity of this prototype alpha-like DNA polymerase. Inhibition of these changes may provide a mechanism for antiherpesvirus drugs.     

Identification of amino acids in herpes simplex virus DNA polymerase involved in substrate and drug recognition.

Herpes simplex virus (HSV) encodes a DNA polymerase that is similar in several respects to the replicative mammalian DNA polymerase alpha. Recently, these and other DNA polymerases have been shown to share several regions of protein sequence similarity. Despite these similarities, antiviral drugs that mimic natural polymerase substrates specifically inhibit herpesvirus DNA polymerases. To study amino acids involved in substrate and drug recognition, we have characterized and mapped altered drug sensitivity markers of nine HSV pol mutants and sequenced the relevant portions of these mutants. The mutations were found to occur within four relatively small regions. One such region, which we designate region A, has sequence similarity only to DNA polymerases that are sensitive to certain antiviral drugs. The other three regions contain sequences that are similar among various DNA polymerases. The multiple mutations occurring within two of these regions make it likely that the regions interact directly with drugs and substrates. Our results lead us to favor a model in which protein folding allows interactions among the four regions to form the substrate and drug binding sites.     

Interaction of herpes simplex virus 1 origin-binding protein with DNA polymerase alpha.

The herpes simplex virus 1 (HSV-1) genome encodes seven polypeptides that are required for its replication. These include a heterodimeric DNA polymerase, a single-strand-DNA-binding protein, a heterotrimeric helicase/primase, and a protein (UL9 protein) that binds specifically to an HSV-1 origin of replication (oris). We demonstrate here that UL9 protein interacts specifically with the 180-kDa catalytic subunit of the cellular DNA polymerase alpha-primase. This interaction can be detected by immunoprecipitation with antibodies directed against either of these proteins, by gel mobility shift of an oris-UL9 protein complex, and by stimulation of DNA polymerase activity by the UL9 protein. These findings suggest that enzymes required for cellular DNA replication also participate in HSV-1 DNA replication.     

Assessing the contribution of the herpes simplex virus DNA polymerase to spontaneous mutations

Background

The thymidine kinase (tk) mutagenesis assay is often utilized to determine the frequency of herpes simplex virus (HSV) replication-mediated mutations. Using this assay, clinical and laboratory HSV-2 isolates were shown to have a 10- to 80-fold higher frequency of spontaneous mutations compared to HSV-1.

Methods

A panel of HSV-1 and HSV-2, along with polymerase-recombinant viruses expressing type 2 polymerase (Pol) within a type 1 genome, were evaluated using the tk and non-HSV DNA mutagenesis assays to measure HSV replication-dependent errors and determine whether the higher mutation frequency of HSV-2 is a distinct property of type 2 polymerases.

Results

Although HSV-2 have mutation frequencies higher than HSV-1 in the tk assay, these errors are assay-specific. In fact, wild type HSV-1 and the antimutator HSV-1 PAA^r5 exhibited a 2–4 fold higher frequency than HSV-2 in the non-HSV DNA mutatagenesis assay. Furthermore, regardless of assay, HSV-1 recombinants expressing HSV-2 Pol had error rates similar to HSV-1, whereas the high mutator virus, HSV-2 6757, consistently showed signficant errors. Additionally, plasmid DNA containing the HSV-2 tk gene, but not type 1 tk or LacZ DNA, was shown to form an anisomorphic DNA stucture.

Conclusions

This study suggests that the Pol is not solely responsible for the virus-type specific differences in mutation frequency. Accordingly, it is possible that (a) mutations may be modulated by other viral polypeptides cooperating with Pol, and (b) the localized secondary structure of the viral genome may partially account for the apparently enhanced error frequency of HSV-2.     

Specific inhibition of herpes simplex virus DNA polymerase by helical peptides corresponding to the subunit interface.

The herpes simplex virus DNA polymerase consists of two subunits--a catalytic subunit and an accessory subunit, UL42, that increases processivity. Mutations affecting the extreme C terminus of the catalytic subunit specifically disrupt subunit interactions and ablate virus replication, suggesting that new antiviral drugs could be rationally designed to interfere with polymerase heterodimerization. To aid design, we performed circular dichroism (CD) spectroscopy and analytical ultracentrifugation studies, which revealed that a 36-residue peptide corresponding to the C terminus of the catalytic subunit folds into a monomeric structure with partial alpha-helical character. CD studies of shorter peptides were consistent with a model where two separate regions of alpha-helix interact to form a hairpin-like structure. The 36-residue peptide and a shorter peptide corresponding to the C-terminal 18 residues blocked UL42-dependent long-chain DNA synthesis at concentrations that had no effect on synthesis by the catalytic subunit alone or by calf thymus DNA polymerase delta and its processivity factor. These peptides, therefore, represent a class of specific inhibitors of herpes simplex virus DNA polymerase that act by blocking accessory-subunit-dependent synthesis. These peptides or their structures may form the basis for the synthesis of clinically effective drugs.     

Extended duration of herpes simplex virus DNA in genital lesions detected by the polymerase chain reaction.

To evaluate the utility of the polymerase chain reaction (PCR) for documenting herpes simplex virus (HSV) in persons with reactivated genital lesions viral isolation was compared with a recently developed PCR method. Three women experiencing four episodes of recurrent genital herpes were followed for 10 days per episode with daily examination and duplicate swabs of the lesions, one for HSV culture and one for PCR. HSV type 2 was cultured from three of four episodes and the mean duration of viral isolation from recurrent genital lesions was 2.6 days. PCR detected HSV DNA from lesion swabs during all four episodes, and HSV DNA was positive for an average of 6.8 days. HSV DNA was demonstrated in ulcerative lesions on 15 of 17 days versus 3 of 17 days by viral isolation (P less than .01). HSV PCR became negative when the lesions reepithelialized. These data suggest that PCR is a more sensitive measure of HSV infection than routine viral culture and that PCR detects the presence of HSV at times when culture is negative.     

Resistance of herpes simplex virus to acycloguanosine: role of viral thymidine kinase and DNA polymerase loci.

Acycloguanosine [9-(2-hydroxyethoxymethyl)guanine; acyclo-Guo] is a potent inhibitor of herpes simplex viruses (HSV); it is selectively phosphorylated in virus-infected cells. In order to define those viral functions that may mediate resistance to acyclo-Guo, the drug sensitivities of temperature-sensitive (ts) and phosphonoacetic acetic acid (PAA)-resistant mutants of HSV-1 and HSV-2 have been determined. Two distinct viral genetic loci are independently associated with acyclo-Guo resistance. Mutations resulting in diminished thymidine kinase activity are associated with resistance to inhibition by acyclo-Guo. Several PAA-resistant viruses that express wild-type levels of thymidine kinase activity are also resistant to acyclo-Guo. This suggests the importance of the viral DNA polymerase region in mediating acyclo-Guo resistance and is consistent with a close relationship between the PAAr mutation site and the AGGr locus. When wild-type HSV-1 is serially propagated under the selective pressure of acyclo-Guo, rapid emergence of resistant virus occurs, accompanied by the simultaneous appearance of thymidine kinase-deficient progeny.     

The herpes simplex virus amplicon: analyses of cis-acting replication functions.

Previous studies have shown that defective virus vectors (amplicons) derived from herpes simplex viruses could be efficiently propagated in virus stocks in the presence of trans-acting helper virus functions. The present study established that two separate cis-acting functions--a DNA replication origin and a cleavage/packaging signal--are required for amplicon propagation. Using deleted derivatives of cloned amplicons, we mapped one of the viral DNA replication origins (ori-2 or oriL) at coordinate 0.422 of the standard HSV-1 genome and at an equivalent position within the HSV-2 genome.     

Expression of herpes simplex virus glycoprotein C from a DNA fragment inserted into the thymidine kinase gene of this virus.

Previous reports have described mutants of herpes simplex virus type 1 that fail to produce or accumulate one of the major glycoproteins, glycoprotein C (gC). This defect is not lethal in cell culture, has been associated with the syncytial plaque morphology of some mutants, and may result from mutations that map to a region on the genome noncontiguous with the structural gene for gC. To investigate the conditions required for, and consequences of, gC expression in a specific genetic background, we have inserted a wild-type allele of the gC gene into the thymidine kinase gene (tk) of a gC- fusion-inducing viral mutant, strain MP. This was accomplished by identifying cloned viral DNA fragments homologous to gC mRNA, inserting the appropriate fragments into the viral tk cloned in pBR322, and then cotransfecting cells with the recombinant plasmids and DNA from strain MP, for selection of insertional TK- mutants. All TK- mutants containing insertions of appropriate sequences (in either orientation) into tk were found to express gC while maintaining the syncytial plaque morphology of strain MP. Elimination of the insertion from one of the TK- mutants was accompanied by loss of ability to produce gC. Our results permit more precise mapping of the DNA sequence encoding gC, to a subfragment of Sal I fragment R (map coordinates 0.620-0.640) and indicate also that promoter sequences for the gC gene may be located in this fragment. Moreover, we can conclude that the previously described regulatory mutation of strain MP does not prevent expression of gC from the DNA inserted into its gene tk and that the syncytial phenotype of MP cannot be due solely to absence of gC.     

A DNA binding protein specific for an origin of replication of herpes simplex virus type 1.

We have identified a protein that binds specifically to an origin of replication (oris) of the herpes simplex virus type 1 genome. The oris binding protein, detectable only in nuclear extracts of infected cells, shows the same time course of appearance as the herpesvirus-induced DNA polymerase and the DNA binding protein ICP8. The partially purified oris binding protein generates a DNase I "footprint" that spans 18- of the 90-base-pair minimal oris sequence. The oris binding protein may, therefore, be analogous to other origin-specific binding proteins that are required for the initiation of viral and chromosomal DNA replication.     

酶联免疫吸附试验和聚合酶链反应检测生殖器标本中的单纯疱疹病毒

目的 评价酶联免疫吸附试验(ELISA)诊断生殖器疱疹的临床应用价值。方法 对120例具有生殖器皮肤、粘膜损害的病人，采用ELISA和分型聚合酶链反应(PCR)检测其生殖器标本中的单纯疱疹病毒(HSV)，两种试验结果不符合者采用第二种PCR检测。结果 120例受检者中，ELISA检出49例HSV阳性，分型PCR检出50例阳性。单纯HSV-1感染者占生殖器疱疹的10.0％，单纯HSV-2感染者占80.0％，HSV-1和HSV-2混合感染者占10.0％。在120例标本中，107例两种试验结果是符合的，13例结果不符合。与“扩大金标准”比较，ELISA的敏感性、特异性、阳性预期值分别为92.0％、95.7％、93.8％，分型PCR的敏感性、特异性、阳性预期值分别为94.0％、95.7％、94.0％。结论 ELISA法检测HSV感染，其敏感性和特异性高，方便、快速，尤其适合大批量样本的检测，值得在临床应用。     

Binding of the herpes simplex virus major regulatory protein to viral DNA.

Infected-cell protein 4 (ICP4), the major regulatory protein specified by herpes simplex virus 1 in infected cells, binds to homologs of the sequence ATCGTCnnnnYCGRC (A sites, where n is any nucleotide, Y is a pyrimidine, and R is a purine) and to unrelated sequences for which no consensus sequence has been derived (B sites). We have examined the binding of ICP4 to each of two A and two B binding sites by using Fab fragments of a monoclonal antibody that is reactive with an epitope located at the N terminus of ICP4 and that decreases the mobility of ICP4-DNA complexes in non-denaturing gels. The results indicate that each type of site binds two monomers of ICP4. Methylation-interference studies on the type B sites mapped the guanines whose methylation interfered with the binding of ICP4. The methylation-interference pattern obtained with one of the B sites was similar to that obtained on an A site but differed from that of the other B site. The ability of ICP4 to bind to DNA fragments containing the binding site appears to be dependent on length and on the proximity of the binding site to the fragment end. Short DNA fragments did not form stable complexes with ICP4 even though they contained all of the purines whose methylation interfered with the binding of the regulatory protein.     

Typing of herpes simplex virus with synthetic DNA probes

Three single-stranded oligonucleotide probes, 22 bases long, homologous to unique regions of herpes simplex virus (HSV) types 1 (HSV-1) and 2 (HSV-2) and a region common to both were chemically synthesized with use of a modified phosphochloridite protocol. For hybridization experiments each probe was labeled with use of polynucleotide kinase and [gamma-32P] ATP to a specific activity of approximately 2 X 10(9) cpm/micrograms. Two hundred one clinical isolates of HSV (96 HSV-1 and 105 HSV-2) collected from vesicles in the mucocutaneous junction of the mouth or from the genital area were analyzed. There was a 99% (199 of 201) agreement between hybridization and monoclonal antibody typing; the two discrepant isolates of HSV-2 that were negative by monoclonal antibody typing were confirmed as HSV-2 by restriction endonuclease analysis. The probes detected between 10(4) and 10(5) HSV infectious units and from 150 to 600 HSV-infected Vero cells. No binding was detected between any of the three probes and isolates of cytomegalovirus, Epstein-Barr virus, and varicella-zoster virus.     

DNA repair proteins affect the lifecycle of herpes simplex virus 1

We report that herpes simplex virus 1 (HSV-1) infection can activate and exploit a cellular DNA damage response that aids viral replication in nonneuronal cells. Early in HSV-1 infection, several members of the cellular DNA damage-sensing machinery are activated and accumulate at sites of viral DNA replication. When this cellular response is abrogated, formation of HSV-1 replication centers is retarded, and viral production is compromised. In neurons, HSV-1 replication centers fail to mature, and the DNA damage response is not initiated. These data suggest that the failure of neurons to mount a DNA damage response to HSV-1 may contribute to the establishment of latency.     

Reconstitution of recombination-dependent DNA synthesis in herpes simplex virus 1

The repair of double-strand DNA breaks by homologous recombination is essential for the maintenance of genome stability. In herpes simplex virus 1, double-strand DNA breaks may arise as a consequence of replication fork collapse at sites of oxidative damage, which is known to be induced upon viral infection. Double-strand DNA breaks are also generated by cleavage of viral a sequences by endonuclease G during genome isomerization. We have reconstituted a system using purified proteins in which strand invasion is coupled with DNA synthesis. In this system, the viral single-strand DNA-binding protein promotes assimilation of single-stranded DNA into a homologous supercoiled plasmid, resulting in the formation of a displacement loop. The 3' terminus of the invading DNA serves as a primer for long-chain DNA synthesis promoted by the viral DNA replication proteins, including the polymerase and helicase-primase. Efficient extension of the invading primer also requires a DNA-relaxing enzyme (eukaryotic topoisomerase I or DNA gyrase). The viral polymerase by itself is insufficient for DNA synthesis, and a DNA-relaxing enzyme cannot substitute for the viral helicase-primase. The viral single-strand DNA-binding protein, in addition to its role in the invasion process, is also required for long-chain DNA synthesis. Form X, a topologically distinct, positively supercoiled form of displacement-loop, does not serve as a template for DNA synthesis. These observations support a model in which recombination and replication contribute toward maintaining viral genomic stability by repairing double-strand breaks. They also account for the extensive branching observed during viral replication in vivo.