UL9 Protein Research Articles

Sequences at the C-terminus of the herpes simplex virus type 1 UL30 protein are dispensable for DNA polymerase activity but not for viral origin-dependent DNA replication.

The UL30 protein of herpes simplex virus type 1 (HSV-1) is a catalytically active DNA polymerase which is present in virus infected cells in a heterodimeric complex with an accessory subunit, the UL42 polypeptide. Both proteins are essential for viral DNA synthesis but because the UL42 protein is much more abundant it has been difficult to determine whether its role is related to, or independent of, its interaction with the UL30 protein in vivo. Since the C-terminal region of UL30 has been shown to be important for interaction with the UL42 protein but dispensable for DNA polymerase activity, a recombinant baculovirus which overexpresses a UL30 protein truncated by 27 amino acids at its C-terminus was constructed and used to assess the significance of the protein-protein interaction. The mutated protein was as active as wildtype (wt) UL30 in a DNA polymerase assay in which activated calf thymus DNA was used as template. However, in contrast to the wt protein, the activity of the truncated polymerase on this template was not stimulated by addition of purified UL42. A monoclonal antibody against the UL42 protein co-precipitated the full length but not truncated polymerase from extracts of cells which had been co-infected with a UL42-expressing recombinant baculovirus. Finally, the truncated protein was not active in a transient assay for HSV-1 origin-dependent DNA replication performed in insect cells in tissue culture. These results indicate that sequences at the C-terminus of the UL30 protein which are dispensable for DNA polymerase activity play essential roles both in viral DNA replication and interaction with the UL42 protein, and strongly suggest that the interaction between the proteins is important in vivo.

The herpes simplex virus type-1 origin binding protein. DNA helicase activity.

The herpes simplex virus type 1 (HSV-1) origin binding protein, the product of the UL9 gene, catalyzes the unwinding of DNA in the 3'-5' direction. Helicase activity is coupled to the hydrolysis of ATP or dATP and to a lesser extent to CTP, dCTP, or UTP. It requires a divalent cation (Mg2+ > Mn2+ > Ca2+) with an optimum at 2.5 mM MgCl2. Activity is optimal at high pH (8.5-9.5) and high temperature (45 degrees C) and is inhibited at ionic strengths > 50 mM NaCl. The helicase activity is specifically stimulated by the HSV-1-encoded single-stranded DNA-binding protein, ICP8, which increases both the rate and extent of helicase activity. Helicase action appears to be stoichiometric, requiring a DNA-dependent assembly of a multimeric UL9 protein complex. Under optimal conditions, the rate of DNA unwinding is approximately 75 base pairs/min.

The conserved helicase motifs of the herpes simplex virus type 1 origin-binding protein UL9 are important for function.

The UL9 gene of herpes simplex virus encodes a protein that specifically recognizes sequences within the viral origins of replication and exhibits helicase and DNA-dependent ATPase activities. The specific DNA binding domain of the UL9 protein was localized to the carboxy-terminal one-third of the molecule (H. M. Weir, J. M. Calder, and N. D. Stow, Nucleic Acids Res. 17:1409-1425, 1989). The N-terminal two-thirds of the UL9 gene contains six sequence motifs found in all members of a superfamily of DNA and RNA helicases, suggesting that this region may be important for helicase activity of UL9. In this report, we examined the functional significance of these six motifs for the UL9 protein through the introduction of site-specific mutations resulting in single amino acid substitutions of the most highly conserved residues within each motif. An in vivo complementation test was used to study the effect of each mutation on the function of the UL9 protein in viral DNA replication. In this assay, a mutant UL9 protein expressed from a transfected plasmid is used to complement a replication-deficient null mutant in the UL9 gene for the amplification of herpes simplex virus origin-containing plasmids. Mutations in five of the six conserved motifs inactivated the function of the UL9 protein in viral DNA replication, providing direct evidence for the importance of these conserved motifs. Insertion mutants resulting in the introduction of two alanines at 100-residue intervals in regions outside the conserved motifs were also constructed. Three of the insertion mutations were tolerated, whereas the other five abolished UL9 function. These data indicate that other regions of the protein, in addition to the helicase motifs, are important for function in vivo. Several mutations result in instability of the mutant products, presumably because of conformational changes in the protein. Taken together, these results suggest that UL9 is very sensitive to mutations with respect to both structure and function, perhaps reflecting its multifunctional character.

Genetic analysis of the herpes simplex virus type 1 UL9 gene: Isolation of a lacZ insertion mutant and expression in eukaryotic cells

HSV-1 host range mutants in complementation group 1–36 (hr27 and hr1 56) whose mutations map in the UL9 gene, encoding the origin binding protein, are unable to form plaques or synthesize viral DNA or late viral proteins when grown in nonpermissive Vero cells (Carmichael, E. P., Kosovsky, M. J., Weller, S. K., 1988, J. Virol. 62, 91–99). These defects are complemented efficiently by growth in the permissive cell line, S22, which contains the wild type version of several HSV genes including UL9. In this report the precise nature and location of the lesions in host range mutants hr27 and hr1 56 were determined by DNA sequencing; both mutants were found to contain identical single-base-pair substitutions at codons 309 and 311 in the UL9 open reading frame. This region lies within the putative helicase domain of the UL9 protein. The UL9 gene was disrupted by the insertion of an insertional mutagen ICP6::lacZ in which the Escherichia coli lacZ gene is expressed under control of the viral ICP6 promoter. Hr94, a viral mutant containing this insertion, does not form plaques or synthesize viral DNA when grown in Vero cells, although both defects are complemented efficiently on permissive cell lines. These results confirm that the UL9 gene product is essential for viral growth and DNA replication. Furthermore, since no detectable UL9 protein is synthesized in hr94-infected cells, this virus provides a useful genetic background for further structure-function analysis since no potentially interfering nonfunctional UL9 protein will be expressed. We have expressed the UL9 open reading frame under the control of the strong and inducible HSV-1 ICP6 promoter and have derived Vero cell lines containing variable copy numbers of the ICP6:: UL9 construct. Cells whose copy number of this construct exceeded approximately 120 are unable to support efficient plaque formation by wild-type virus. Cell lines with low copy numbers of this construct are able to complement hr27, hr1 56, and hr94.

The UL8 subunit of the herpes simplex virus helicase-primase complex is required for efficient primer utilization.

The herpes simplex virus (HSV) type 1 helicase-primase is a three-protein complex, consisting of a 1:1:1 association of UL5, UL8, and UL52 gene products (J.J. Crute, T. Tsurumi, L. Zhu, S. K. Weller, P. D. Olivo, M. D. Challberg, E. S. Mocarski, and I. R. Lehman, Proc. Natl. Acad. Sci. USA 86:2186-2189, 1989). We have purified this complex, as well as a subcomplex consisting of UL5 and UL52 proteins, from insect cells infected with baculovirus recombinants expressing the appropriate gene products. In confirmation of previous reports, we find that whereas UL5 alone has greatly reduced DNA-dependent ATPase activity, the UL5/UL52 subcomplex retains the activities characteristic of the heterotrimer: DNA-dependent ATPase activity, DNA helicase activity, and the ability to prime DNA synthesis on a poly(dT) template. We also found that the primers made by the subcomplex are equal in length to those synthesized by the UL5/UL8/UL52 complex. In an effort to uncover a role for UL8 in HSV DNA replication, we have developed a model system for lagging-strand synthesis in which the primase activity of the helicase-primase complex is coupled to the activity of the HSV DNA polymerase on ICP8-coated single-stranded M13 DNA. Using this assay, we found that the UL8 subunit of the helicase-primase is critical for the efficient utilization of primers; in the absence of UL8, we detected essentially no elongation of primers despite the fact that the rate of primer synthesis on the same template is undiminished. Reconstitution of lagging-strand synthesis in the presence of UL5/UL52 was achieved by the addition of partially purified UL8. Essentially identical results were obtained when Escherichia coli DNA polymerase I was substituted for the HSV polymerase/UL42 complex. On the basis of these findings, we propose that UL8 acts to increase the efficiency of primer utilization by stabilizing the association between nascent oligoribonucleotide primers and template DNA.

The effect of the UL42 protein on the DNA polymerase activity of the catalytic subunit of the DNA polymerase encoded by herpes simplex virus type 1

The effect that the UL42 protein of herpes simplex virus type 1 has on the DNA polymerase activity of the DNA polymerase catalytic subunit (Pol) of the same virus has been investigated. The observed effects are critically dependent on the salt used and its concentration, such that the UL42 protein may inhibit, have little or no effect on, or activate the Pol activity, depending on the conditions used. The observed effects are due to the values for K m app for activated DNA and V max app for Pol and the Pol-UL42 protein complex differently varying with salt concentration.

Triple-helix formation is compatible with an adjacent DNA-protein complex.

The effect of oligonucleotide-directed triple-helix formation on the binding of a protein to an immediately adjacent sequence has been examined. A double-stranded oligonucleotide was designed with a target site for the binding of a pyrimidine oligonucleotide located immediately adjacent to the recognition sequence for the herpes simplex virus type 1 (HSV-1) origin of replication binding protein, which is encoded by the UL9 gene of HSV-1. Since the optimal conditions for the binding of the UL9 protein and the pyrimidine oligonucleotide to the duplex DNA are markedly different, a pyrimidine oligonucleotide was designed to optimize binding affinity and specificity for the target duplex oligonucleotide. Consideration was given to length and sequence composition in an effort to maximize triple-strand formation under conditions amenable to the formation of the UL9-DNA complex. Using gel mobility shift assays, a trimolecular complex composed of duplex DNA bound to both a third oligonucleotide strand and the UL9 protein was detected, indicating that the UL9-DNA complex is compatible with the presence of a triple helix in the immediately adjacent sequences.

Herpes simplex virus type 1 origin-dependent DNA replication in insect cells using recombinant baculoviruses.

The minimal set of seven herpes simplex virus type 1 (HSV-1) genes required for viral origin-dependent DNA synthesis was previously identified using a transient replication assay in a mammalian cell line permissive for HSV-1 growth. We have constructed recombinant baculoviruses which efficiently express the products of each of these seven genes in infected Spodoptera frugiperda (Sf) insect cells. When Sf cells were transfected with a plasmid containing a functional HSV-1 origin of replication, and subsequently superinfected with a mixture of these seven viruses, the input plasmid was amplified. This amplification exhibited properties characteristic of genuine HSV-1 DNA replication: all seven HSV-1 replication gene products were required, replicated DNA was detected as concatemers, and mutated origins were impaired to similar extents in insect cells and cells permissive for HSV-1 replication. These results demonstrate that the HSV-1 proteins expressed in Sf cells are fully competent for viral DNA synthesis, and indicate that any host function essential in mammalian cells must also be present in the infected insect cells. This system also provides a convenient method by which mutated replication proteins can be screened for function and produced in amounts sufficient for biochemical studies. Using this approach we show that the ability of the UL9 protein to bind to the viral origins of replication is not sufficient for it to facilitate DNA synthesis.

Nucleoprotein complex formed between herpes simplex virus UL9 protein and the origin of DNA replication: inter- and intramolecular interactions.

The UL9 gene of herpes simplex virus type 1 encodes an origin-binding protein. UL9 protein purified from baculovirus vector-infected insect cells forms a stable complex with DNA containing the herpes simplex virus origin of DNA replication, oriS. Contained within oriS are two UL9 protein-binding sites, I and II, bracketing an (A + T)-rich region. UL9 protein, visualized by electron microscopy, binds selectively at the site of the origin and covers approximately 120 base pairs. Upon formation of the nucleoprotein complex, the apparent contour length of the DNA is shortened, suggesting that this amount of DNA is wrapped or condensed by the protein. A nucleoprotein complex of similar size and structure forms on an inactive origin deleted for binding site II. Multiple intermolecular interactions occur. In particular, UL9 nucleoprotein complexes interact in trans with other UL9 nucleoprotein complexes such that dimer DNA molecules are formed with a junction at the position of protein binding. The DNA molecules in these intermolecular complexes are aligned predominantly in a parallel orientation.

Isolation of a herpes simplex virus type 1 mutant deleted for the essential UL42 gene and characterization of its null phenotype

We isolated a cell line, designated V9, stably transformed with the herpes simplex virus type 1 (HSV-1) UL42 gene, which is one of seven genes required in trans for the replication of plasmids containing an HSV origin of replication (C. A. Wu, N. J. Nelson, D. J. McGeoch, and M. D. Challberg, J. Virol. 62:435-443, 1988). V9 cells inducibly expressed the product of the UL42 gene, the 65-kDa DNA-binding protein (65KDBP), and were used as a permissive host to construct a mutant virus deleted for this essential gene. The UL42 deletion mutant, designated Cgal delta 42, displayed a tight early phenotype in nonpermissive Vero cells producing no infectious progeny, viral DNA, or late gene products but accumulated selected immediate-early and early transcripts with kinetics similar to those of wild-type virus. Wild-type levels of viral DNA and infectious progeny were produced in permissive V9 cells, despite the fact that V9 cells infected with Cgal delta 42 accumulated less than 1% of the UL42 RNA and protein found in Cgal+ virus-infected V9 or Vero cells. These results indicate that only small quantities of the 65KDBP are required for the synthesis of HSV DNA and the production of infectious virus. Although we could find no evidence that the superinduction of the 65KDBP in V9 cells infected with Cgal+ repressed expression of HSV-1 genes as observed in cells expressing another DNA-binding protein, ICP8 (P. K. Orberg and P. A. Schaffer, J. Virol. 61:1136-1146, 1987), the induction of the 65KDBP in V9 cells correlated with an approximately 2-h-earlier shift in the expression of genes from all three kinetic classes. The availability of the UL42 mutant should facilitate the construction of more subtle UL42 mutants which will be useful in the elucidation of the interrelationship between the 65KDBP and other DNA replication proteins as well as in the characterization of additional important functional domains.

A novel functional domain of an alpha-like DNA polymerase. The binding site on the herpes simplex virus polymerase for the viral UL42 protein.

Most DNA-dependent DNA polymerases exist as a complex with one or more noncovalently bound accessory proteins, whose presence is necessary for the correct functioning of the holoenzyme. Using the herpes simplex virus DNA polymerase as a representative member of the alpha-polymerase family, we have recreated the association between the polymerase and its accessory protein UL42 in vitro through the translation in rabbit reticulocyte lysate of bacteriophage RNA polymerase-generated transcripts encoding the two polypeptides. Study of the ability of deleted versions of the polymerase protein to bind UL42, as detected by coimmunoprecipitation of the two polypeptides, defined a carboxyl-terminal region of the DNA polymerase that was both necessary and sufficient for the association. This domain is distinct from regions of the protein previously characterized as involved in catalysis. The results suggest a strategy for the design of novel targeted antiviral drugs, which would disrupt the DNA polymerase-UL42 complex.

Analysis of the binding sites for the varicella-zoster virus gene 51 product within the viral origin of DNA replication

The C-terminal 322 amino acids of the varicella-zoster virus (VZV) gene 51 product were expressed in Escherichia coli and shown to bind to specific DNA sequences within the VZV origin of DNA replication. The gene 51 product and its herpes simplex virus type 1 homolog (the UL9 protein) are capable of recognizing identical DNA sequences but the arrangement of binding sites within the origin regions of the two viruses differs. Three binding sites for the VZV gene 51 protein were identified within the VZV origin region and these lie in the same orientation and on the same side of the origin palindromic DNA sequence. DNA replication assays in transfected tissue culture cells demonstrated that the site closest to the palindrome is essential for origin activity whereas the most distal site is dispensable. The middle binding site may play an auxiliary role in DNA synthesis.

Functional interaction between the herpes simplex-1 DNA polymerase and UL42 protein.

The herpes simplex virus 1 (HSV-1) UL42 protein, one of seven herpes-encoded polypeptides that are required for the replication of the HSV-1 genome, is found in a 1:1 complex with the HSV-1 DNA polymerase (Crute, J. J., and Lehman, I. R. (1989) J. Biol. Chem. 264, 19266-19270). To obtain herpes DNA polymerase free of UL42 protein, we have cloned and overexpressed the Pol gene in a recombinant baculovirus vector and purified the recombinant DNA polymerase to near homogeneity. Replication of singly primed M13mp18 single-stranded DNA by the recombinant enzyme in the presence of the herpes encoded single-stranded DNA-binding protein ICP8 yields in addition to some full-length product a distribution of intermediate length products by a quasi-processive mode of deoxynucleotide polymerization. Addition of the purified UL42 protein results in completely processive polymerization and the generation of full-length products. Similar processivity is observed with the HSV-1 DNA polymerase purified from herpes-infected Vero cells. Processive DNA replication by the DNA polymerase isolated from HSV-1-infected Vero cells or the recombinant DNA polymerase-UL42 protein complex requires that the single-stranded DNA be coated with saturating levels of ICP8. ICP8 which binds single-stranded DNA in a highly cooperative manner is presumably required to melt out regions of secondary structure in the single-stranded DNA template, thereby potentiating the processivity enhancing action of the UL42 protein.

Two binding sites for the herpes simplex virus type 1 UL9 protein are required for efficient activity of the oriS replication origin

Two sites within the short region origin of DNA replication (oriS) in herpes simplex virus type 1 (HSV-1) which bind the product of the UL9 gene have previously been identified. One of these sites (site I) contains an 11 bp sequence which is also present in oriS of varicella-zoster virus, and the other (site II) includes a related element differing in two positions. A third sequence (motif III), which lies close to binding site I, differs from the site I element at only a single position. We have deleted specifically each of these three 11 bp sequences from within functional copies of HSV-1 oriS and have examined the effects on origin activity and binding of the UL9 protein. Gel retardation analyses confirmed the important roles of the regions deleted from sites I and II in interacting with the UL9 protein. In transient replication assays, copies of oriS lacking the site I or II elements exhibited undetectable or residual (4 to 8%) activity respectively. The UL9 protein did not bind to motif III even in the absence of site I sequences, although removal of the motif III sequence caused a small reduction in oriS activity. A single base change which converted the sequence within binding site I to that of motif III was sufficient to abolish both the interaction of the UL9 gene product at this locus and the replicative ability of oriS. Therefore, interaction of the UL9 protein with binding site I is essential for origin activity, but the presence of binding site II is also required for efficient replication.

Herpes simplex virus helicase-primase: the UL8 protein is not required for DNA-dependent ATPase and DNA helicase activities

The herpes simplex virus type 1 helicase-primase complex consists of the products of the UL5, UL8 and UL52 genes. We have expressed these proteins in insect cells using baculovirus vectors and studied the requirements for enzymatic activities associated with the DNA unwinding function of the complex. In agreement with a recent report (Dodson, M.S., Crute, J.J., Bruckner, R.C. and Lehman, I.R. 1989, J. Biol. Chem. 264, 20835-20838) we find that DNA-dependent ATPase and DNA helicase activities are assembled in vivo in insect cells triply infected with viruses expressing the UL5, UL8 and UL52 proteins. Moreover, these activities were also detected in cells in which only the UL5 and UL52 products were expressed indicating that the presence of the UL8 protein is essential for neither the ATPase nor helicase activity of the complex.

Herpes simplex virus DNA replication: the UL9 gene encodes an origin-binding protein.

Herpes simplex virus 1 contains seven genes that are necessary and sufficient for origin-dependent DNA synthesis in cultured cells. We have expressed the product of one of these genes, UL9, in insect cells by using a baculovirus expression vector. The apparent size of the UL9 protein, both in insect cells and in herpes simplex virus-infected Vero cells, is 82,000 Da. By using an immunoassay for protein-DNA interaction, we have shown that UL9 protein binds specifically to the herpes simplex virus origins of DNA replication, oriS and oriL. DNase I "footprint" analysis has shown that the UL9 protein interacts with two related sites on oriS, located on each arm of a nearly perfect palindrome. Our data strongly suggest that the origin-binding activity described previously by Elias et al. [Elias, P., O'Donnell, M. E., Mocarski, E. S. & Lehman, I. R. (1986) Proc. Natl. Acad. Sci. USA 83, 6322-6326] is the product of the UL9 gene.