The human cytomegalovirus UL44 C clamp wraps around DNA

Processivity factors tether the catalytic subunits of DNA polymerases to DNA so that continuous synthesis of long DNA strands is possible. The human cytomegalovirus DNA polymerase subunit UL44 forms a C clamp-shaped dimer intermediate in structure between monomeric herpes simplex virus UL42, which binds DNA directly via a basic surface, and the trimeric sliding clamp PCNA, which encircles DNA. To investigate how UL44 interacts with DNA, calculations were performed in which a 12 bp DNA oligonucleotide was docked to UL44. The calculations suggested that UL44 encircles DNA, which interacts with basic residues both within the cavity of the C clamp and in flexible loops of UL44 that complete the "circle." The results of mutational and crosslinking studies were consistent with this model. Thus, UL44 is a "hybrid" of UL42 and PCNA: its structure is intermediate between the two and its mode of interaction with DNA has elements of both.     

Crystal Structure of Epstein-Barr Virus DNA Polymerase Processivity Factor BMRF1

The DNA polymerase processivity factor of the Epstein-Barr virus, BMRF1, associates with the polymerase catalytic subunit, BALF5, to enhance the polymerase processivity and exonuclease activities of the holoenzyme. In this study, the crystal structure of C-terminally truncated BMRF1 (BMRF1-ΔC) was solved in an oligomeric state. The molecular structure of BMRF1-ΔC shares structural similarity with other processivity factors, such as herpes simplex virus UL42, cytomegalovirus UL44, and human proliferating cell nuclear antigen. However, the oligomerization architectures of these proteins range from a monomer to a trimer. PAGE and mutational analyses indicated that BMRF1-ΔC, like UL44, forms a C-shaped head-to-head dimer. DNA binding assays suggested that basic amino acid residues on the concave surface of the C-shaped dimer play an important role in interactions with DNA. The C95E mutant, which disrupts dimer formation, lacked DNA binding activity, indicating that dimer formation is required for DNA binding. These characteristics are similar to those of another dimeric viral processivity factor, UL44. Although the R87E and H141F mutants of BMRF1-ΔC exhibited dramatically reduced polymerase processivity, they were still able to bind DNA and to dimerize. These amino acid residues are located near the dimer interface, suggesting that BMRF1-ΔC associates with the catalytic subunit BALF5 around the dimer interface. Consequently, the monomeric form of BMRF1-ΔC probably binds to BALF5, because the steric consequences would prevent the maintenance of the dimeric form. A distinctive feature of BMRF1-ΔC is that the dimeric and monomeric forms might be utilized for the DNA binding and replication processes, respectively.     

Crystal structure of the cytomegalovirus DNA polymerase subunit UL44 in complex with the C terminus from the catalytic subunit. Differences in structure and function relative to unliganded UL44

The human cytomegalovirus DNA polymerase is composed of a catalytic subunit, UL54, and an accessory protein, UL44, which has a structural fold similar to that of other processivity factors, including herpes simplex virus UL42 and homotrimeric sliding clamps such as proliferating cell nuclear antigen. Several specific residues in the C-terminal region of UL54 and in the "connector loop" of UL44 are required for the association of these proteins. Here, we describe the crystal structure of residues 1-290 of UL44 in complex with a peptide from the extreme C terminus of UL54, which explains this interaction at a molecular level. The UL54 peptide binds to structural elements similar to those used by UL42 and the sliding clamps to associate with their respective binding partners. However, the details of the interaction differ from those of other processivity factor-peptide complexes. Crucial residues include a three-residue hydrophobic "plug" from the UL54 peptide and Ile(135) of UL44, which forms a critical intramolecular hydrophobic anchor for interactions between the connector loop and the peptide. As was the case for the unliganded UL44 structure, the UL44-peptide complex forms a head-to-head dimer that could potentially form a C-shaped clamp on DNA. However, the peptide-bound structure displays subtle differences in the relative orientation of the two subdomains of the protein, resulting in a more open clamp, which we predicted would affect its association with DNA. Indeed, filter binding assays revealed that peptide-bound UL44 binds DNA with higher affinity. Thus, interaction with the catalytic subunit appears to affect both the structure and function of UL44.     

The crystal structure of an unusual processivity factor, herpes simplex virus UL42, bound to the C terminus of its cognate polymerase

Herpes simplex virus DNA polymerase is a heterodimer composed of a catalytic subunit, Pol, and an unusual processivity subunit, UL42, which, unlike processivity factors such as PCNA, directly binds DNA. The crystal structure of a complex of the C-terminal 36 residues of Pol bound to residues 1-319 of UL42 reveals remarkable similarities between UL42 and PCNA despite contrasting biochemical properties and lack of sequence homology. Moreover, the Pol-UL42 interaction resembles the interaction between the cell cycle regulator p21 and PCNA. The structure and previous data suggest that the UL42 monomer interacts with DNA quite differently than does multimeric toroidal PCNA. The details of the structure lead to a model for the mechanism of UL42, provide the basis for drug design, and allow modeling of other proteins that lack sequence homology with UL42 or PCNA.     

The herpes simplex virus processivity factor, UL42, binds DNA as a monomer

The processivity subunit of the herpes simplex virus DNA polymerase, UL42, is a monomer in solution. However, UL42 is structurally similar to sliding clamp processivity factors, such as PCNA, which encircle DNA as a multimeric ring. We used chemical crosslinking and electrophoretic mobility-shift assays to investigate whether UL42 oligomerizes upon DNA binding. UL42 did not form intermolecular crosslinks upon treatment with glutaraldehyde in the presence of DNA, whereas proteins that are known to be multimers in solution were successfully crosslinked by this treatment. This result suggests that UL42 does not form multimers on DNA. We next analyzed the composition of UL42:DNA complexes using electrophoretic mobility-shift assays. UL42 was mixed with a maltose-binding protein-UL42 fusion protein before being added to DNA. The patterns of electrophoretic mobility of the resultant protein:DNA complexes were those predicted if each isoform of UL42 binds to DNA as a monomer. From this result and the failure of UL42 to form crosslinks, we infer that UL42 binds DNA as a monomer.     

Binding parameters and thermodynamics of the interaction of the human cytomegalovirus DNA polymerase accessory protein, UL44, with DNA: implications for the processivity mechanism

The mechanisms of processivity factors of herpesvirus DNA polymerases remain poorly understood. The proposed processivity factor for human cytomegalovirus DNA polymerase is a DNA-binding protein, UL44. Previous findings, including the crystal structure of UL44, have led to the hypothesis that UL44 binds DNA as a dimer via lysine residues. To understand how UL44 interacts with DNA, we used filter-binding and electrophoretic mobility shift assays and isothermal titration calorimetry (ITC) analysis of binding to oligonucleotides. UL44 bound directly to double-stranded DNA as short as 12bp, with apparent dissociation constants in the nanomolar range for DNAs >18bp, suggesting a minimum DNA length for UL44 interaction. UL44 also bound single-stranded DNA, albeit with lower affinity, and for either single- or double-stranded DNA, there was no apparent sequence specificity. ITC analysis revealed that UL44 binds to duplex DNA as a dimer. Binding was endothermic, indicating an entropically driven process, likely due to release of bound ions. Consistent with this hypothesis, analysis of the relationship between binding and ionic strength indicated that, on average, 4±1 monovalent ions are released in the interaction of each monomer of UL44 with DNA. The results taken together reveal interesting implications for how UL44 may mediate processivity.     

Three-dimensional structure of the beta subunit of E. coli DNA polymerase III holoenzyme: a sliding DNA clamp.

The crystal structure of the beta subunit (processivity factor) of DNA polymerase III holoenzyme has been determined at 2.5 A resolution. A dimer of the beta subunit (M(r) = 2 x 40.6 kd, 2 x 366 amino acid residues) forms a ring-shaped structure lined by 12 alpha helices that can encircle duplex DNA. The structure is highly symmetrical, with each monomer containing three domains of identical topology. The charge distribution and orientation of the helices indicate that the molecule functions by forming a tight clamp that can slide on DNA, as shown biochemically. A potential structural relationship is suggested between the beta subunit and proliferating cell nuclear antigen (PCNA, the eukaryotic polymerase delta [and epsilon] processivity factor), and the gene 45 protein of the bacteriophage T4 DNA polymerase.     

Linear diffusion on DNA despite high-affinity binding by a DNA polymerase processivity factor.

The oligomeric "sliding clamp" processivity factors, such as PCNA, are thought to rely on a loose, topological association with DNA to slide freely along dsDNA. Unlike PCNA, the processivity subunit of the herpes simplex virus DNA polymerase, UL42, is a monomer and has an intrinsic affinity for dsDNA that is remarkably high for a sequence-independent DNA binding protein. Using a DNase footprinting assay, we demonstrate that UL42 translocates with the catalytic subunit of the polymerase during chain elongation. In addition, footprinting and electrophoretic mobility shift assays show that, despite its tight DNA binding, UL42 is capable of linear diffusion on DNA at a rate of between 17 and 47 bp/s. Our results thus suggest that, despite profound biochemical differences with the sliding clamps, UL42 can freely slide downstream with the catalytic subunit during DNA replication.     

The Crystal Structure of PF-8, the DNA Polymerase Accessory Subunit from Kaposi's Sarcoma-Associated Herpesvirus

Kaposi''s sarcoma-associated herpesvirus is an emerging pathogen whose mechanism of replication is poorly understood. PF-8, the presumed processivity factor of Kaposi''s sarcoma-associated herpesvirus DNA polymerase, acts in combination with the catalytic subunit, Pol-8, to synthesize viral DNA. We have solved the crystal structure of residues 1 to 304 of PF-8 at a resolution of 2.8 Å. This structure reveals that each monomer of PF-8 shares a fold common to processivity factors. Like human cytomegalovirus UL44, PF-8 forms a head-to-head dimer in the form of a C clamp, with its concave face containing a number of basic residues that are predicted to be important for DNA binding. However, there are several differences with related proteins, especially in loops that extend from each monomer into the center of the C clamp and in the loops that connect the two subdomains of each protein, which may be important for determining PF-8''s mode of binding to DNA and to Pol-8. Using the crystal structures of PF-8, the herpes simplex virus catalytic subunit, and RB69 bacteriophage DNA polymerase in complex with DNA and initial experiments testing the effects of inhibition of PF-8-stimulated DNA synthesis by peptides derived from Pol-8, we suggest a model for how PF-8 might form a ternary complex with Pol-8 and DNA. The structure and the model suggest interesting similarities and differences in how PF-8 functions relative to structurally similar proteins.Most if not all organisms with DNA genomes have mechanisms to ensure processive DNA synthesis. In bacteria, archaea, and eukaryotes, DNA polymerase subunits include a catalytic subunit and a processivity factor, often referred to as a “sliding clamp.” In these organisms, a clamp loader protein is required to assemble the processivity factor onto the DNA (27, 37). The bacterial sliding (beta) clamp is made up of homodimers of a subunit that comprises three structurally similar subdomains (26), whereas archaeal and eukaryotic proliferating cell nuclear antigen (PCNA) is composed of homotrimers that comprise two structurally similar subdomains (27, 37). For both of these clamps, the monomers assemble head-to-tail to form a closed homodimeric or homotrimeric ring, respectively, around the DNA. In these organisms, a clamp loader protein is required to efficiently load the clamp onto DNA, using an ATP-dependent process. Once loaded on DNA, the processivity factor is capable of binding directly to the DNA polymerase, conferring extended strand synthesis without falling off of the template (50).Herpesviruses encode their own DNA polymerases. However, unlike bacteria, archaea, and eukaryotes, herpesviruses do not encode clamp loaders to assemble their processivity factors onto the DNA. Yet, the accessory subunits of the herpesvirus DNA polymerases still associate with DNA with nanomolar affinity to enable long-chain DNA synthesis (9, 16, 23, 25, 29, 35, 44, 46, 53, 56). Human herpesviruses are divided into three classes, namely, the alpha-, beta-, and gammaherpesviruses, based on homologies found in their genomic organization as well as in protein sequences and function (45). Crystal structures have been determined for the processivity factor UL42 from the alphaherpesvirus herpes simplex virus type 1 (HSV-1) and for UL44 from the betaherpesvirus human cytomegalovirus (HCMV) (2, 3, 58). Despite having little if any sequence homology with processivity factors outside of their herpesvirus subfamily, these structures all share the “processivity fold” originally seen in the structure of the bacterial beta clamp (26). Interestingly, some of these processivity factors have a different quaternary structure. PCNA forms a head-to-tail trimeric ring (18, 27), HSV-1 UL42 is a monomer (10, 14, 16, 46, 58) equivalent to one-third of the PCNA complex, and HCMV UL44 is a head-to-head dimer in the form of a C-shaped clamp (2, 3, 9).Both HSV-1 UL42 and HCMV UL44 have a basic face that has been shown to be important for interacting with DNA (25, 35). In the case of dimeric HCMV UL44, the basic surface of each monomer faces inward, toward the center of the C clamp, and includes a basic loop, called the “gap loop,” that is thought to wrap around DNA (24). Recently the crystal structure of the bacterial beta clamp was determined in complex with DNA (15). In that structure, DNA was found to be located in the central pore of the clamp. Amino acid residues that interacted with DNA were in positions structurally homologous to those found on the positively charged faces of UL42 and UL44.UL42 and UL44 each also has a surface, facing away from the DNA binding face, that is important for interacting with the catalytic subunit of the viral DNA polymerase. Indeed, both of these proteins have been crystallized in complex with C-terminal peptides from their respective catalytic subunits, HSV-1 UL30 and HCMV UL54 (2, 58). Together with biochemical and mutational analyses, these crystal structures indicated that, although the details of the interaction are different, the catalytic subunit of the polymerase binds to a region including and in close proximity to a long loop that connects the N- and C-terminal subdomains, called the interdomain connector loop (32-34). The corresponding region of PCNA is also important for polymerase attachment and mediates the interactions of PCNA with many other cellular proteins (40). Both UL54 and UL30 were shown to attach to their respective subunits, UL44 and UL42, by way of their extreme C termini. The C-terminal residues responsible for this interaction correspond to amino acids that are not detectably conserved, either by sequence or by structure, among herpesvirus catalytic subunits. The HSV-1 UL30-UL42 interaction involves a groove to one side of the UL42 connector loop, with hydrophilic interactions being critical (58). The HCMV UL54-UL44 interaction involves a crevice near the UL44 connector loop, and hydrophobic interactions are crucial (2, 32, 33). Moreover, the HCMV UL44 crevice is on the opposite side of the connector loop with respect to the HSV-1 UL42 groove.Kaposi''s sarcoma-associated herpesvirus (KSHV), a gammaherpesvirus, encodes a viral DNA polymerase catalytic subunit, Pol-8, and an accessory subunit, PF-8 (4, 7, 8, 29, 48, 57). PF-8 can bind to Pol-8 directly and specifically (8, 29) and is required for long-chain DNA synthesis in vitro (29). Similarly to UL44, PF-8 forms dimers in solution and when bound to DNA (9). Although it is likely that UL44 and PF-8 are the processivity factors for HCMV and KSHV, respectively, rigorous experiments demonstrating this have not been performed. However, for the sake of brevity and clarity, we will refer to these proteins as processivity factors.Here we present the crystal structure of PF-8 and show that PF-8 forms a head-to-head homodimer akin to UL44 but lacking the long gap loops which are thought to wrap around DNA. This suggests that PF-8 binds DNA differently than does UL44 or UL42. Because Pol-8 appears to lack a long, flexible C-terminal tail with a length comparable to those of other herpesvirus Pols, we expect the mode of binding of the catalytic subunit to be different as well. Based on structural data, information from homologs, and initial biochemical results, we were able to identify possible sites for interactions with DNA and Pol-8 and to propose a model for the simultaneous interaction of all three components of the complex. Further, the availability of crystal structures for all three herpesvirus classes provides new insights into comparative structure, function, and evolution.     

Human Kaposi's sarcoma herpesvirus processivity factor-8 functions as a dimer in DNA synthesis

In the absence of other proteins, the DNA polymerase (Pol-8) of Kaposi's sarcoma herpesvirus incorporates only several nucleotides from a primer template. However, association with the Kaposi's sarcoma herpesvirus processivity factor (PF-8) enables Pol-8 to incorporate thousands of nucleotides. Unlike the well described sliding clamp processivity factors, eukaryotic proliferating cell nuclear antigen and Escherichia coli beta-subunit, PF-8 and other herpesvirus processivity factors do not require a clamp loader or ATP to bind to template DNA. To begin to understand the mechanism used by PF-8 to achieve processivity, we have now purified PF-8 and demonstrated that it is a dimer both in solution and on the DNA. Mutational analysis of the PF-8 protein (396R) indicates that residues between 277 and 304 as well as the N-terminal 21 amino acids are required for dimerization. The results further correlate PF-8 dimerization with binding to Pol-8 and stabilizing Pol-8 on primer template. Notably, although removal of only 26 residues from the C terminus of PF-8 does not affect its ability to form dimers on DNA or to bind Pol-8, only short DNA chains (<100 nucleotides) are synthesized. This indicates that full-length PF-8 is necessary to enable Pol-8 to incorporate thousands of nucleotides. Interestingly, cross-linking of the processivity factor UL44 of cytomegalovirus reveals that it is a dimer in solution also.     

Specific residues in the connector loop of the human cytomegalovirus DNA polymerase accessory protein UL44 are crucial for interaction with the UL54 catalytic subunit

The human cytomegalovirus DNA polymerase includes an accessory protein, UL44, which has been proposed to act as a processivity factor for the catalytic subunit, UL54. How UL44 interacts with UL54 has not yet been elucidated. The crystal structure of UL44 revealed the presence of a connector loop analogous to that of the processivity subunit of herpes simplex virus DNA polymerase, UL42, which is crucial for interaction with its cognate catalytic subunit, UL30. To investigate the role of the UL44 connector loop, we replaced each of its amino acids (amino acids 129 to 140) with alanine. We then tested the effect of each substitution on the UL44-UL54 interaction by glutathione S-transferase pulldown and isothermal titration calorimetry assays, on the stimulation of UL54-mediated long-chain DNA synthesis by UL44, and on the binding of UL44 to DNA-cellulose columns. Substitutions that affected residues 133 to 136 of the connector loop measurably impaired the UL44-UL54 interaction without altering the ability of UL44 to bind DNA. One substitution, I135A, completely disrupted the binding of UL44 to UL54 and inhibited the ability of UL44 to stimulate long-chain DNA synthesis by UL54. Thus, similar to the herpes simplex virus UL30-UL42 interaction, a residue of the connector loop of the accessory subunit is crucial for UL54-UL44 interaction. However, while alteration of a polar residue of the UL42 connector loop only partially reduced binding to UL30, substitution of a hydrophobic residue of UL44 completely disrupted the UL54-UL44 interaction. This information may aid the discovery of small-molecule inhibitors of the UL44-UL54 interaction.     

Inhibition of human cytomegalovirus DNA polymerase by C-terminal peptides from the UL54 subunit

In common with other herpesviruses, the human cytomegalovirus (HCMV) DNA polymerase contains a catalytic subunit (Pol or UL54) and an accessory protein (UL44) that is thought to increase the processivity of the enzyme. The observation that antisense inhibition of UL44 synthesis in HCMV-infected cells strongly inhibits viral DNA replication, together with the structural similarity predicted for the herpesvirus processivity subunits, highlights the importance of the accessory protein for virus growth and raises the possibility that the UL54/UL44 interaction might be a valid target for antiviral drugs. To investigate this possibility, overlapping peptides spanning residues 1161 to 1242 of UL54 were synthesized and tested for inhibition of the interaction between purified UL54 and UL44 proteins. A peptide, LPRRLHLEPAFLPYSVKAHECC, corresponding to residues 1221 to 1242 at the very C terminus of UL54, disrupted both the physical interaction between the two proteins and specifically inhibited the stimulation of UL54 by UL44. A mutant peptide lacking the two carboxy-terminal cysteines was markedly less inhibitory, suggesting a role for these residues in the UL54/UL44 interaction. Circular dichroism spectroscopy indicated that the UL54 C-terminal peptide can adopt a partially alpha-helical structure. Taken together, these results indicate that the two subunits of HCMV DNA polymerase most likely interact in a way which is analogous to that of the two subunits of herpes simplex virus DNA polymerase, even though there is no sequence homology in the binding site, and suggest that the UL54 peptide, or derivatives thereof, could form the basis for developing a new class of anti-HCMV inhibitors that act by disrupting the UL54/UL44 interaction.     

Structural and functional similarities of prokaryotic and eukaryotic DNA polymerase sliding clamps.

The remarkable processivity of cellular replicative DNA polymerases derive their tight grip to DNA from a ring-shaped protein that encircles DNA and tethers the polymerase to the chromosome. The crystal structures of prototypical 'sliding clamps' of prokaryotes (beta subunit) and eukaryotes (PCNA) are ring shaped proteins for encircling DNA. Although beta is a dimer and PCNA is a trimer, their structures are nearly superimposable. Even though they are not hexamers, the sliding clamps have a pseudo 6-fold symmetry resulting from three globular domains comprising each beta monomer and two domains comprising each PCNA monomer. These domains have the same chain fold and are nearly identical in three-dimensions. The amino acid sequences of 11 beta and 13 PCNA proteins from different organisms have been aligned and studied to gain further insight into the relation between the structure and function of these sliding clamps. Furthermore, a putative embryonic form of PCNA is the size of beta and thus may encircle DNA as a dimer like the prokaryotic clamps.     

Effects of substitutions of arginine residues on the basic surface of herpes simplex virus UL42 support a role for DNA binding in processive DNA synthesis

The way that UL42, the processivity subunit of the herpes simplex virus DNA polymerase, interacts with DNA and promotes processivity remains unclear. A positively charged face of UL42 has been proposed to participate in electrostatic interactions with DNA that would tether the polymerase to a template without preventing its translocation via DNA sliding. An alternative model proposes that DNA binding by UL42 is not important for processivity. To investigate these issues, we substituted alanine for each of four conserved arginine residues on the positively charged surface. Each single substitution decreased the DNA binding affinity of UL42, with 14- to 30-fold increases in apparent dissociation constants. The mutant proteins exhibited no meaningful change in affinity for binding to the C terminus of the catalytic subunit of the polymerase, indicating that the substitutions exert a specific effect on DNA binding. The substitutions decreased UL42-mediated long-chain DNA synthesis by the polymerase in the same rank order in which they affected DNA binding, consistent with a role for DNA binding in polymerase processivity. Combining these substitutions decreased DNA binding further and impaired the complementation of a UL42 null virus in transfected cells. Additionally, using a revised mathematical model to analyze rates of dissociation of UL42 from DNAs of various lengths, we found that dissociation from internal sites, which would be the most important for tethering the polymerase, was relatively slow, even at ionic strengths that permit processive DNA synthesis by the holoenzyme. These data provide evidence that the basic surface of UL42 interacts with DNA and support a model in which DNA binding by UL42 is important for processive DNA synthesis.     

Structure of a sliding clamp on DNA

The structure of the E. coli beta clamp polymerase processivity factor has been solved in complex with primed DNA. Interestingly, the clamp directly binds the DNA duplex and also forms a crystal contact with the ssDNA template strand, which binds into the protein-binding pocket of the clamp. We demonstrate that these clamp-DNA interactions function in clamp loading, perhaps by inducing the ring to close around DNA. Clamp binding to template ssDNA may also serve to hold the clamp at a primed site after loading or during switching of multiple factors on the clamp. Remarkably, the DNA is highly tilted as it passes through the beta ring. The pronounced 22 degrees angle of DNA through beta may enable DNA to switch between multiple factors bound to a single clamp simply by alternating from one protomer of the ring to the other.     

Replication factor C is a more effective proliferating cell nuclear antigen (PCNA) opener than the checkpoint clamp loader, Rad24-RFC

Clamp loaders from all domains of life load clamps onto DNA. The clamp tethers DNA polymerases to DNA to increase the processivity of synthesis as well as the efficiency of replication. Here, we investigated proliferating cell nuclear antigen (PCNA) binding and opening by the Saccharomyces cerevisiae clamp loader, replication factor C (RFC), and the DNA damage checkpoint clamp loader, Rad24-RFC, using two separate fluorescence intensity-based assays. Analysis of PCNA opening by RFC revealed a two-step reaction in which RFC binds PCNA before opening PCNA rather than capturing clamps that have transiently and spontaneously opened in solution. The affinity of RFC for PCNA is about an order of magnitude lower in the absence of ATP than in its presence. The affinity of Rad24-RFC for PCNA in the presence of ATP is about an order magnitude weaker than that of RFC for PCNA, similar to the RFC-PCNA interaction in the absence of ATP. Importantly, fewer open clamp loader-clamp complexes are formed when PCNA is bound by Rad24-RFC than when bound by RFC.     

Mutations That Increase DNA Binding by the Processivity Factor of Herpes Simplex Virus Affect Virus Production and DNA Replication Fidelity

The interactions of the herpes simplex virus processivity factor UL42 with the catalytic subunit of the viral polymerase (Pol) and DNA are critical for viral DNA replication. Previous studies, including one showing that substitution of glutamine residue 282 with arginine (Q282R) results in an increase of DNA binding in vitro, have indicated that the positively charged back surface of UL42 interacts with DNA. To investigate the biological consequences of increased DNA binding by UL42 mutations, we constructed two additional UL42 mutants, including one with a double substitution of alanine for aspartic acid residues (D270A/D271A) and a triple mutant with the D270A/D271A and Q282R substitutions. These UL42 mutants exhibited increased and prolonged DNA binding without an effect on binding to a peptide corresponding to the C terminus of Pol. Plasmids expressing any of the three UL42 mutants with an increased positive charge on the back surface of UL42 were qualitatively competent for complementation of growth and DNA replication of a UL42 null mutant on Vero cells. We then engineered viruses expressing these mutant proteins. The UL42 mutants were more resistant to detergent extraction than wild-type UL42, suggesting that they are more tightly associated with DNA in infected cells. All three UL42 mutants formed smaller plaques on Vero cells and replicated to reduced yields compared with results for a control virus expressing wild-type UL42. Moreover, mutants with double and triple mutations, which contain D270A/D271A mutations, exhibited increased mutation frequencies, and mutants containing the Q282R mutation exhibited elevated ratios of virion DNA copies per PFU. These results suggest that herpes simplex virus has evolved so that UL42 neither binds DNA too tightly nor too weakly to optimize virus production and replication fidelity.Processivity factors of DNA polymerases promote long-chain DNA synthesis by preventing dissociation of the DNA polymerase from the primer/template. Processivity factors also can influence DNA replication fidelity, as indicated by numerous in vivo and in vitro studies (1-3, 5, 6, 11, 12, 18, 28, 36). A major class of processivity factors known as “sliding clamps” includes proliferating cell nuclear antigen (PCNA) of eukaryotic cells (23) and gp45 of T4 bacteriophage (27). Sliding clamps are homodimers or homotrimers that encircle DNA and interact with the catalytic subunits (Pols) of their cognate DNA polymerases to promote processive DNA synthesis.A second class of processivity factors includes those encoded by herpesviruses and is exemplified by herpes simplex virus (HSV) UL42. UL42 forms a heterodimer with the HSV Pol. Both subunits are essential for production of infectious virus and for viral DNA replication (20, 26). UL42 can stimulate long-chain DNA synthesis by Pol, and template challenge experiments established that this stimulation is due to increased processivity (15). In addition to its interaction with Pol, which is mediated by the C terminus of Pol, UL42 also binds DNA directly with high affinity (14, 15, 30, 37). This mode of DNA binding differs from that of sliding clamps, which do not form high-affinity direct interactions with DNA (13) but must be loaded onto DNA with the aid of ATP-dependent clamp loaders for their normal functioning (16). Nevertheless, the structure of UL42 is very similar to a monomer of the sliding clamp PCNA (39). Like other processivity factors, UL42 also plays a role in maintaining DNA replication fidelity both in vivo and in vitro (5, 18).The “back face” (opposite face to the side that binds Pol) of a UL42 molecule contains several positively charged residues. By titrating the effects of cations on UL42 DNA binding, it was determined that charge-charge interactions are involved in the interaction (22). Substitutions of alanine for any of four arginine residues on the back face of UL42 resulted in substantial reductions in DNA binding without affecting the binding to peptide corresponding to the C terminus of Pol in vitro (31), while substitutions of lysine for arginine had little or no effect on DNA binding affinity (22). A UL42 mutant (Q282R) containing a substitution of arginine for a negatively charged glutamine residue on the back face of UL42 exhibited a fourfold increase in DNA binding without altering the interaction with the Pol C-terminal peptide in vitro (22). Therefore, the positively charged surface of UL42 is important for the interaction between UL42 and DNA. A question raised by these studies is whether UL42 could bind DNA so tightly as to affect HSV replication.Mutant viruses engineered to encode individual arginine-to-alanine substitution mutations in UL42 exhibit several phenotypes, including a delayed onset of viral DNA replication, reduced virus yields, and reduced fidelity of DNA replication (18). Recombinant viruses expressing UL42 with multiple substitutions of alanine for arginine residues exhibit even greater effects on viral DNA replication and virus yields (19). Thus, reducing DNA binding by UL42 deleteriously affects viral growth and DNA replication fidelity. However, these studies did not address whether increasing DNA binding by UL42 would have any effects on viral DNA replication, replication fidelity, or virus production.In this study we engineered two new UL42 mutant proteins (with the D270A/D271A or Q282R/D270A/D271A mutations) that contain less negative charge on the back face and examined the effects of these substitutions on DNA and Pol peptide binding. In addition, recombinant viruses were constructed to examine the effect of these multiple substitutions and the single Q282R substitution on virus production, DNA replication, and the fidelity of DNA replication.     

Identification of crucial hydrogen-bonding residues for the interaction of herpes simplex virus DNA polymerase subunits via peptide display, mutational, and calorimetric approaches

The catalytic subunit, Pol, of herpes simplex virus DNA polymerase interacts via its extreme C terminus with the processivity subunit, UL42. This interaction is critical for viral replication and thus a potential target for antiviral drug action. To investigate the Pol-binding region on UL42, we engineered UL42 mutations but also used random peptide display to identify artificial ligands of the Pol C terminus. The latter approach selected ligands with homology to residues 171 to 176 of UL42. Substitution of glutamine 171 with alanine greatly impaired binding to Pol and stimulation of long-chain DNA synthesis by Pol, identifying this residue as crucial for subunit interactions. To study these interactions quantitatively, we used isothermal titration calorimetry and wild-type and mutant forms of Pol-derived peptides and UL42. Each of three peptides corresponding to either the last 36, 27, or 18 residues of Pol bound specifically to UL42 in a 1:1 complex with a dissociation constant of 1 to 2 microM. Thus, the last 18 residues suffice for most of the binding energy, which was due mainly to a change in enthalpy. Substitutions at positions corresponding to Pol residue 1228 or 1229 or at UL42 residue 171 abolished or greatly reduced binding. These residues participate in hydrogen bonds observed in the crystal structure of the C terminus of Pol bound to UL42. Thus, interruption of these few bonds is sufficient to disrupt the interaction, suggesting that small molecules targeting the relevant side chains could interfere with Pol-UL42 binding.