Stepwise Evolution of the Herpes Simplex Virus Origin Binding Protein and Origin of Replication

The herpes simplex virus replicon consists of cis-acting sequences, oriS and oriL, and the origin binding protein (OBP) encoded by the UL9 gene. Here we identify essential structural features in the initiator protein OBP and the replicator sequence oriS, and we relate the appearance of these motifs to the evolutionary history of the alphaherpesvirus replicon. Our results reveal two conserved sequence elements in herpes simplex virus type 1, OBP; the RVKNL motif, common to and specific for all alphaherpesviruses, is required for DNA binding, and the WP XXXGAXXFXX L motif, found in a subset of alphaherpesviruses, is required for specific binding to the single strand DNA-binding protein ICP8. A 121-amino acid minimal DNA binding domain containing conserved residues is not soluble and does not bind DNA. Additional sequences present 220 amino acids upstream from the RVKNL motif are needed for solubility and function. We also examine the binding sites for OBP in origins of DNA replication and how they are arranged. NMR and DNA melting experiments demonstrate that origin sequences derived from many, but not all, alphaherpesviruses can adopt stable boxI/boxIII hairpin conformations. Our results reveal a stepwise evolutionary history of the herpes simplex virus replicon and suggest that replicon divergence contributed to the formation of major branches of the herpesvirus family.Herpesviruses have been found in animal species ranging from molluscs to man. According to the International Committee on Taxonomy of Viruses, the order of Herpesvirales consists of three families as follows: Alloherpesviridae, Herpesviridae, and Malacoherpesviridae (1). The subfamilies Alphaherpesvirinae, Betaherpesvirinae, and Gammaherpesvirinae are found within the family of Herpesviridae. The events leading to establishment of a new virus species are poorly understood, but in the case of herpesviruses it is commonly assumed that viruses co-evolve with their hosts (2). Herpesviruses have thus become well adapted to their hosts and may reside in a latent state in the host for a lifetime with little or no overt signs of infection. Upon reactivation, the infectious virus will be released. The viruses remain faithful to their hosts, and infections across species borders are rare but may under specific circumstances give rise to fatal disease.Replication of herpes simplex virus type 1 (HSV-1),² requires a cis-acting DNA sequence, the replicator, termed oriS or oriL, an initiator protein, OBP or UL9 protein, and a replisome composed of DNA polymerase, helicase-primase, and a single strand DNA-binding protein referred to as ICP8 or UL29 protein (3). OBP assisted by ICP8 can in an ATP-dependent reaction unwind double-stranded oriS (4, 5). The resulting single-stranded DNA adopts a hairpin conformation, which is stably bound by OBP (6, 7). The herpesvirus replisome once assembled on DNA is capable of synthesizing leading and lagging strands processively in a coordinated fashion (8). DNA replication is likely to start on circular molecules produced by the action of DNA ligase IV/XRCC4 and proceed in a θ-type manner (9, 10). Later, a rolling circle mode of replication dominates giving rise to characteristic head-to-tail concatemers. The initiator protein OBP appears to be strictly required only during the first few hours of the infectious cycle (11, 12).The HSV-1 origin binding protein was first isolated using an assay monitoring specific binding to HSV-1 oriS (13). A minimal DNA-binding site was identified using footprinting techniques as well as binding studies with double-stranded oligonucleotides (14). For alphaherpesviruses the high affinity binding site is always TTCGCAC, with a minor exception for CHV1 also referred to as monkey B virus (3 The C-terminal 317 amino acids of alphaherpesvirus OBP can be isolated as a soluble protein, which remains capable of high affinity binding to the sequence TTCGCAC (15). The C-terminal domain of HSV-1 OBP, here referred to as ΔOBP, binds as a monomer to the major groove in the DNA and makes contacts with base pairs as well as the deoxyribose-phosphate backbone (16, 17). ΔOBP binds DNA specifically with an estimated K_d of 0.3 nm, a value that is highly influenced by the composition of the assay buffer (16). At high protein concentrations ΔOBP form aggregates, which, still in a sequence-specific manner, binds DNA (16). A number of studies have attempted to define amino acids involved in DNA binding (18–21). In addition, sequence comparisons between alphaherpesviruses and roseoloviruses have helped to identify amino acids in OBP potentially involved in DNA binding as well as corresponding recognition sequences in origins of DNA replication (22–25). However, a comprehensive and quantitative study of evolutionarily conserved amino acids required for DNA binding is still lacking.

TABLE 1

Functionally significant sequence motifs for herpes simplex virus replicon evolutionOrigins of DNA replication have been identified from sequence analysis. For roseoloviruses the sequences for two slightly different binding sites for OBP have been listed (31). The number and orientation of OBP-binding sites in relation to an AT-rich spacer sequence are schematically presented by symbols > and <. Note that since a virus often has more than one origin of replication they may exist as variants. This is indicated by symbols within parentheses. The conserved amino acids within the ICP8-binding motif are shown in boldface type. Sources and nomenclature for DNA sequences have been presented in Footnote 3.Open in a separate windowThe single strand DNA-binding protein, ICP8 encoded by the UL29 gene, is involved in initiation of DNA replication, and it also participates in the elongation phase at the replication fork (4, 5, 26). ICP8 forms a specific complex with OBP (26, 27). Studies with deletion mutants have demonstrated that important sequences are found close to the C terminus of OBP, but amino acids directly participating in the high affinity interaction have not been identified. The interaction is biologically significant, because deletion of the extreme C terminus enhances the helicase activity of OBP but reduces origin-dependent DNA synthesis (26).The HSV-1 oriS contains three copies of the binding site for OBP; two binding sites, box I and box II, are high affinity sites, and the third binding site, box III, has a very low affinity for OBP (14) (Fig. 1). All sites are required for efficient replication, and in a competitive situation there is a strong selection for the most efficient replicator sequence (28). Box III and box I are arranged in a palindrome, which becomes rearranged upon activation to form an alternative conformation, most likely a hairpin (4, 6, 7). Point mutations that prevent formation of a hairpin reduce replication, and compensatory mutations restore complementary base pairing as well as the ability to replicate (7).Open in a separate windowFIGURE 1.Schematic presentation of the herpes simplex virus replicon. Upper part, HSV-1 oriS. The linear genome contains three homologous replication origins, two copies of oriS and one copy oriL, and encodes seven replication proteins. Middle part, HSV-1 OBP. OBP or UL9 protein is a superfamily II DNA helicase as well as a sequence-specific DNA-binding protein. Here the helicase domain is represented by two connected ellipsoids, and the C-terminal DNA binding is drawn as a circle. The OBP-binding sites in oriS are shown. The OBP dimer binds two double-stranded DNA box I oligonucleotides but only one hairpin with a single-stranded tail (48). The figure is intended to demonstrate conformational changes affecting the DNA binding domain, referred to as ΔOBP, during activation of oriS. Lower part, DNA binding domain ΔOBP. A schematic presentation of the following three motifs discussed in this publication: the F553 XX KYL motif required for proper folding of the DNA binding domain, the R756VKNL motif necessary for DNA binding, and the W839PXXXGAXXFXXL motif involved in binding to ICP8.To learn more about the mechanism of virus evolution, we have examined the evolutionary history of some functionally significant features of the HSV-1 replicon and related them to a sequence-based evolutionary tree. The results indicate that replicon divergence, characterized by the stepwise appearance of the DNA-binding RVKNL motif, the WPXXXGAXXFXXL ICP8-binding motif, and the boxIII–boxI palindrome, may have played important roles in establishing major branches of the alphaherpesvirus tree.