Bacteriophage T4 DNA Replication Research Articles

DNA Polymerase‐Parental DNA Interaction is Essential for Helicase‐Polymerase Coupling in Bacteriophage T7 DNA Replication

DNA helicase and polymerase work cooperatively at the replication fork to unwind the parental DNA and perform leading strand DNA synthesis. It was believed that the helicase migrates at the forefront of the replication fork and unwinds DNA to provide a template for DNA polymerase. Although extensively investigated, the molecular basis of the helicase‐polymerase coupling is not fully understood. Replisome from bacteriophage T7 has been a model system for estimating mechanisms of DNA replication. Recently, the first structure of the helicase‐polymerase complex at a replication fork was reported with the T7 system. The T7 replisome structure suggested that the helicase and polymerase sandwich the parental DNA, with each enzyme pulling one daughter strand in opposite directions. Interestingly, it is the T7 polymerase but not helicase that carries the parental DNA with a β‐hairpin loop stacking at the fork opening and a positively charged cleft that holds the parental DNA. However, the role of the polymerase‐parental DNA interaction in helicase‐polymerase coupling has not been investigated. Here, we created and characterized T7 polymerases with perturbed β‐hairpin loop and the positively charged cleft. Mutations on both structural elements significantly reduced the strand displacement synthesis by T7 polymerase but had a minor effect on DNA synthesis against linear DNA substrate. Moreover, the mutations eliminate synergistic helicase polymerase binding to the DNA fork substrate and replication fork progression in mobility shift assay and rolling‐circle replication assays. Our biochemical data suggested that polymerase plays a dominant role in helicase‐polymerase coupling and replisome progression.

DNA Polymerase-Parental DNA Interaction Is Essential for Helicase-Polymerase Coupling during Bacteriophage T7 DNA Replication.

DNA helicase and polymerase work cooperatively at the replication fork to perform leading-strand DNA synthesis. It was believed that the helicase migrates to the forefront of the replication fork where it unwinds the duplex to provide templates for DNA polymerases. However, the molecular basis of the helicase-polymerase coupling is not fully understood. The recently elucidated T7 replisome structure suggests that the helicase and polymerase sandwich parental DNA and each enzyme pulls a daughter strand in opposite directions. Interestingly, the T7 polymerase, but not the helicase, carries the parental DNA with a positively charged cleft and stacks at the fork opening using a β-hairpin loop. Here, we created and characterized T7 polymerases each with a perturbed β-hairpin loop and positively charged cleft. Mutations on both structural elements significantly reduced the strand-displacement synthesis by T7 polymerase but had only a minor effect on DNA synthesis performed against a linear DNA substrate. Moreover, the aforementioned mutations eliminated synergistic helicase-polymerase binding and unwinding at the DNA fork and processive fork progressions. Thus, our data suggested that T7 polymerase plays a dominant role in helicase-polymerase coupling and replisome progression.

Combined Solution and Crystal Methods Reveal the Electrostatic Tethers That Provide a Flexible Platform for Replication Activities in the Bacteriophage T7 Replisome.

Recent structural studies of the bacteriophage T7 DNA replication system have shed light on how multiple proteins assemble to copy two antiparallel DNA strands. In T7, acidic C-terminal tails of both the primase-helicase and single-stranded DNA binding protein bind to two basic patches on the DNA polymerase to aid in replisome assembly, processivity, and coordinated DNA synthesis. Although these electrostatic interactions are essential for DNA replication, the molecular details for how these tails bind the polymerase are unknown. We have determined an X-ray crystal structure of the T7 DNA polymerase bound to both a primer/template DNA and a peptide that mimics the C-terminal tail of the primase-helicase. The structure reveals that the essential C-terminal phenylalanine of the tail binds to a hydrophobic pocket that is surrounded by positive charge on the surface of the polymerase. We show that alterations of polymerase residues that engage the tail lead to defects in viral replication. In the structure, we also observe dTTP bound in the exonuclease active site and stacked against tryptophan 160. Using both primer/extension assays and high-throughput sequencing, we show how mutations in the exonuclease active site lead to defects in mismatch repair and an increase in the level of mutagenesis of the T7 genome. Finally, using small-angle X-ray scattering, we provide the first solution structures of a complex between the single-stranded DNA binding protein and the DNA polymerase and show how a single-stranded DNA binding protein dimer engages both one and two copies of DNA polymerase.

Using Site Specific Fluorescent Probes to Examine Replication Fork Destabilization by Regulatory Proteins of the Bacteriophage T4 DNA Replication Complex

The reconstituted T4 DNA replication complex serves as the simplest model system to examine the ‘core’ replication mechanisms of higher organisms. In this study we used site-specifically introduced fluorescent base analogues to track local conformational changes of the nucleic acid bases, as well as Cy3/Cy5 dye-pairs inserted into the sugar-phosphate backbones to monitor backbone motions at defined positions within the DNA during interactions of the fork with regulatory proteins. By combining low energy circular dichroism (CD) and fluorescent measurements of the site-specifically introduced fluorescent base analogues with single molecule (sm) FRET experiments with cyanine dyes, we have monitored the binding stoichiometries and interactions of the regulatory proteins with model replication fork constructs. The assembly pathways and binding stoichiometries of gp59 (the helicase loader protein), gp41 (the hexameric helicase) and gp61 (the primase) were studied using functional assays as well as single molecule imaging experiments. The results showed that the stoichiometry of gp59/gp41/gp61 subunits within the functional complex is 1:6:1. CD and fluorescence experiments with base analogue probes show that gp59 preferentially binds to and perturbs the bases at the junction of a forked DNA construct, and that the addition of the gp41 helicase hexamer extends this conformational perturbation deep into the DNA duplex. In contrast, the addition of gp61 perturbs the bases at the fork junction, but not base-pairs deep in the duplex sequence. Based on these results and our previous studies we propose a possible model for DNA duplex unwinding by the helicase loader-primosome-single-strand binding protein complex within the T4 replication system.

Binding of the Single-Stranded DNA Binding Protein (gp32) of T4 Bacteriophage Induces Position-Specific Local Conformational Changes in DNA Lattices that can be Monitored by Fluorescent Probes

The single-stranded (ss) DNA binding protein (gp32) of the bacteriophage T4 DNA replication system plays a major role in integrating the functions of the sub-assemblies of the replication complex by interacting with different replication proteins. Substitution of fluorescent base analogues at defined positions in nucleic acid constructs can be used to study local conformational changes of the nucleic acid bases at specific sites, and Cy3/Cy5 dye-pairs inserted into the sugar-phosphate backbones can track the backbone motions of the DNA lattice during gp32 binding. By monitoring the fluorescence, circular dichroism, absorbance and FRET signals of these base and backbone probes, equilibrium and dynamic measurements can provide information about the molecular details of replication mechanisms. In the present study we use 6-methyl isoxanthopterin (6-MI), a fluorescent base analogue of guanine, to monitor local conformational changes of DNA lattices on gp32 binding. We find that aromatic amino acid residues of gp32 stacks with the bases of ssDNA lattices, depending on the specific positions of the bases within the binding domain of the gp32 molecule, and that Molecular Dynamics simulations are consistent with the experimental results. These results may shed light on how the hydrophobic pockets found in many protein-nucleic acid interaction complexes may stabilize the intercalation or stacking of aromatic amino acid residues with nucleic acid bases. Using internally labeled cyanine dyes, we have also investigated the double-stranded DNA melting properties of gp32 protein at a replication fork junction, and our results suggest that gp32 can enhance breathing at a fork junction if the ssDNA arm at the fork is of sufficient length to permit formation of cooperatively-bound gp32 clusters at the junction.

Mechanistic Studies of DNA-Protein Interactions in Bacteriophage T4 DNA Replication Complexes at Single-Base Resolution

Combining biophysical measurements on the function and control of T4 bacteriophage replication complexes with detailed structural information can throw light onto the mechanism of action of these ‘macromolecular machines’. In this study we use the low energy circular dichroism and fluorescent properties of site-specifically introduced fluorescent base analogues to monitor the binding and interactions of gene 32 protein (gp32), the ssDNA binding protein of the T4 DNA replication complex, and gene 59 protein (gp59), the helicase loader protein involved in loading the T4 primosome complex onto replication forks. We show that gp32 binds preferentially to the 3'-end of a short ssDNA oligomer and that only two or three nucleotide bases at the 3' end are directly perturbed by the binding interaction, although the binding site size in the polynucleotide binding mode is 7 nts. Loss of exciton coupling in the CD spectrum and an increase in fluorescence intensity shows that gp32 binding causes extension of the sugar-phosphate backbone of the oligonucleotide. Mechanisms involved in gp32 binding to its ssDNA targets in both the isolated and the cooperative binding modes will be described. In addition our CD and fluorescence experiments with base analogue probes show the gp59 binding to a forked DNA construct perturbs the bases at the junction and suggests that once gp41 is loaded the perturbation extends deep into the double helix. Mechanisms whereby these proteins work in tandem in setting up various functional interactions with the other components of the DNA replication complex will be discussed.

Mechanistic Studies of DNA-Protein Interactions in Bacteriophage T4 DNA Replication Complexes at Single-Base Resolution

Mechanistic Studies of DNA-Protein Interactions in Bacteriophage T4 DNA Replication Complexes at Single-Base Resolution

Role of the LEXE Motif of Protein-primed DNA Polymerases in the Interaction with the Incoming Nucleotide

The LEXE motif, conserved in eukaryotic type DNA polymerases, is placed close to the polymerization active site. Previous studies suggested that the second Glu was involved in binding a third noncatalytic ion in bacteriophage RB69 DNA polymerase. In the protein-primed DNA polymerase subgroup, the LEXE motif lacks the first Glu in most cases, but it has a conserved Phe/Trp and a Gly preceding that position. To ascertain the role of those residues, we have analyzed the behavior of mutants at the corresponding ϕ29 DNA polymerase residues Gly-481, Trp-483, Ala-484, and Glu-486. We show that mutations at Gly-481 and Trp-483 hamper insertion of the incoming dNTP in the presence of Mg(2+) ions, a reaction highly improved when Mn(2+) was used as metal activator. These results, together with previous crystallographic resolution of ϕ29 DNA polymerase ternary complex, allow us to infer that Gly-481 and Trp-483 could form a pocket that orients Val-250 to interact with the dNTP. Mutants at Glu-486 are also defective in polymerization and, as mutants at Gly-481 and Trp-483, in the pyrophosphorolytic activity with Mg(2+). Recovery of both reactions with Mn(2+) supports a role for Glu-486 in the interaction with the pyrophosphate moiety of the dNTP.

Thioredoxin, the Processivity Factor, Sequesters an Exposed Cysteine in the Thumb Domain of Bacteriophage T7 DNA Polymerase

Gene 5 protein (gp5) of bacteriophage T7 is a non-processive DNA polymerase. It achieves processivity by binding to Escherichia coli thioredoxin (trx). gp5/trx complex binds tightly to a primer-DNA template enabling the polymerization of hundreds of nucleotides per binding event. gp5 contains 10 cysteines. Under non-reducing condition, exposed cysteines form intermolecular disulfide linkages resulting in the loss of polymerase activity. No disulfide linkage is detected when Cys-275 and Cys-313 are replaced with serines. Cys-275 and Cys-313 are located on loop A and loop B of the thioredoxin binding domain, respectively. Replacement of either cysteine with serine (gp5-C275S, gp5-C313S) drastically decreases polymerase activity of gp5 on dA(350)/dT(25). On this primer-template gp5/trx in which Cys-313 or Cys-275 is replaced with serine have 50 and 90%, respectively, of the polymerase activity observed with wild-type gp5/trx. With single-stranded M13 DNA as a template gp5-C275S/trx retains 60% of the polymerase activity of wild-type gp5/trx. In contrast, gp5-C313S/trx has only one-tenth of the polymerase activity of wild-type gp5/trx on M13 DNA. Both wild-type gp5/trx and gp5-C275S/trx catalyze the synthesis of the entire complementary strand of M13 DNA, whereas gp5-C313S/trx has difficulty in synthesizing DNA through sites of secondary structure. gp5-C313S fails to form a functional complex with trx as measured by the apparent binding affinity as well as by the lack of a physical interaction with thioredoxin during hydroxyapatite-phosphate chromatography. Small angle x-ray scattering reveals an elongated conformation of gp5-C313S in comparison to a compact and spherical conformation of wild-type gp5.

Assembly and subunit stoichiometry of the functional helicase-primase (primosome) complex of bacteriophage T4

Physical biochemical techniques are used to establish the structure, subunit stoichiometry, and assembly pathway of the primosome complex of the bacteriophage T4 DNA replication system. Analytical ultracentrifugation and fluorescence anisotropy methods show that the functional T4 primosome consists of six gp41 helicase subunits that assemble into a hexagon, driven by the binding of six NTPs (or six nonhydrolyzable GTPγS analogues) that are located at and stabilize the intersubunit interfaces, together with a single tightly bound gp61 primase subunit. Assembling the components of the primosome onto a model DNA replication fork is a multistep process, but equilibrium cannot be reached along all mixing pathways. Producing a functional complex requires that the helicase hexamer be assembled in the presence of the DNA replication fork construct prior to the addition of the primase to avoid the formation of metastable DNA-protein aggregates. The gp41 helicase hexamer binds weakly to fork DNA in the absence of primase, but forms a much more stable primosome complex that expresses full and functional helicase (and primase) activities when bound to a gp61 primase subunit at a helicase:primase subunit ratio of 61. The presence of additional primase subunits does not change the molecular mass or helicase activity of the primosome, but significantly inhibits its primase activity. We develop both an assembly pathway and a minimal mechanistic model for the structure and function of the T4 primosome that are likely to be relevant to the assembly and function of the replication primosome subassemblies of higher organisms as well.

Choreography of bacteriophage T7 DNA replication

The replication system of phage T7 provides a model for DNA replication. Biochemical, structural, and single-molecule analyses together provide insight into replisome mechanics. A complex of polymerase, a processivity factor, and helicase mediates leading strand synthesis. Establishment of the complex requires an interaction of the C-terminal tail of the helicase with the polymerase. During synthesis the complex is stabilized by other interactions to provide for a processivity of 5 kilobase (kb). The C-terminal tail also interacts with a distinct region of the polymerase to captures dissociating polymerase to increase the processivity to >17kb. The lagging strand is synthesized discontinuously within a loop that forms and resolves during each cycle of Okazaki fragment synthesis. The synthesis of a primer as well as the termination of a fragment signal loop resolution.

Position-Specific DNA Base Pair ‘BREATHING’ at the Replication Fork Junction Regulates Helicase Access

We previously used near UV circular dichroism and fluorescence spectroscopy of DNA base analogues to measure position-specific DNA ‘breathing’ fluctuations at model replication fork DNA constructs (Jose et al., PNAS, 106, 4231, 2009). Building on that study we have now site-specifically inserted 2-aminopurine bases into such constructs on both sides of the fork junction as spectroscopic probes to monitor specific interactions with an unwinding helicase in ‘real time’. The tight-binding, stable and highly active primosome assembly of the bacteriophage T4 DNA replication system was used as the helicase, and was formed into an active unwinding initiation complex by assembling T4 helicase and primase subunits in a 6:1 subunit ratio in the presence of the non-hydrolyzable GTP-analogue, GTPγS. (The addition of hydrolyzable GTP to this initiation complex results in complete unwinding of the model replication fork.) The binding of this helicase initiation complex at the replication fork, primarily via backbone contacts with the leading strand, traps the first breathing base pair of the fork in an open conformation. The other base and base pair positions were examined to map the interactions of the bound helicase on both sides of the fork. These results suggest that this replication helicase unwinds DNA by a primarily ‘passive’ mechanism, with unwinding depending on DNA breathing.

Initiation of bacteriophage T4 DNA replication and replication fork dynamics: a review in the Virology Journal series on bacteriophage T4 and its relatives.

Bacteriophage T4 initiates DNA replication from specialized structures that form in its genome. Immediately after infection, RNA-DNA hybrids (R-loops) occur on (at least some) replication origins, with the annealed RNA serving as a primer for leading-strand synthesis in one direction. As the infection progresses, replication initiation becomes dependent on recombination proteins in a process called recombination-dependent replication (RDR). RDR occurs when the replication machinery is assembled onto D-loop recombination intermediates, and in this case, the invading 3' DNA end is used as a primer for leading strand synthesis. Over the last 15 years, these two modes of T4 DNA replication initiation have been studied in vivo using a variety of approaches, including replication of plasmids with segments of the T4 genome, analysis of replication intermediates by two-dimensional gel electrophoresis, and genomic approaches that measure DNA copy number as the infection progresses. In addition, biochemical approaches have reconstituted replication from origin R-loop structures and have clarified some detailed roles of both replication and recombination proteins in the process of RDR and related pathways. We will also discuss the parallels between T4 DNA replication modes and similar events in cellular and eukaryotic organelle DNA replication, and close with some current questions of interest concerning the mechanisms of replication, recombination and repair in phage T4.

Structural analysis of bacteriophage T4 DNA replication: a review in the Virology Journal series on bacteriophage T4 and its relatives.

The bacteriophage T4 encodes 10 proteins, known collectively as the replisome, that are responsible for the replication of the phage genome. The replisomal proteins can be subdivided into three activities; the replicase, responsible for duplicating DNA, the primosomal proteins, responsible for unwinding and Okazaki fragment initiation, and the Okazaki repair proteins. The replicase includes the gp43 DNA polymerase, the gp45 processivity clamp, the gp44/62 clamp loader complex, and the gp32 single-stranded DNA binding protein. The primosomal proteins include the gp41 hexameric helicase, the gp61 primase, and the gp59 helicase loading protein. The RNaseH, a 5' to 3' exonuclease and T4 DNA ligase comprise the activities necessary for Okazaki repair. The T4 provides a model system for DNA replication. As a consequence, significant effort has been put forth to solve the crystallographic structures of these replisomal proteins. In this review, we discuss the structures that are available and provide comparison to related proteins when the T4 structures are unavailable. Three of the ten full-length T4 replisomal proteins have been determined; the gp59 helicase loading protein, the RNase H, and the gp45 processivity clamp. The core of T4 gp32 and two proteins from the T4 related phage RB69, the gp43 polymerase and the gp45 clamp are also solved. The T4 gp44/62 clamp loader has not been crystallized but a comparison to the E. coli gamma complex is provided. The structures of T4 gp41 helicase, gp61 primase, and T4 DNA ligase are unknown, structures from bacteriophage T7 proteins are discussed instead. To better understand the functionality of T4 DNA replication, in depth structural analysis will require complexes between proteins and DNA substrates. A DNA primer template bound by gp43 polymerase, a fork DNA substrate bound by RNase H, gp43 polymerase bound to gp32 protein, and RNase H bound to gp32 have been crystallographically determined. The preparation and crystallization of complexes is a significant challenge. We discuss alternate approaches, such as small angle X-ray and neutron scattering to generate molecular envelopes for modeling macromolecular assemblies.

Two Modes of Interaction of the Single-stranded DNA-binding Protein of Bacteriophage T7 with the DNA Polymerase-Thioredoxin Complex

The DNA polymerase encoded by bacteriophage T7 has low processivity. Escherichia coli thioredoxin binds to a segment of 76 residues in the thumb subdomain of the polymerase and increases the processivity. The binding of thioredoxin leads to the formation of two basic loops, loops A and B, located within the thioredoxin-binding domain (TBD). Both loops interact with the acidic C terminus of the T7 helicase. A relatively weak electrostatic mode involves the C-terminal tail of the helicase and the TBD, whereas a high affinity interaction that does not involve the C-terminal tail occurs when the polymerase is in a polymerization mode. T7 gene 2.5 single-stranded DNA-binding protein (gp2.5) also has an acidic C-terminal tail. gp2.5 also has two modes of interaction with the polymerase, but both involve the C-terminal tail of gp2.5. An electrostatic interaction requires the basic residues in loops A and B, and gp2.5 binds to both loops with similar affinity as measured by surface plasmon resonance. When the polymerase is in a polymerization mode, the C terminus of gene 2.5 protein interacts with the polymerase in regions outside the TBD. gp2.5 increases the processivity of the polymerase-helicase complex during leading strand synthesis. When loop B of the TBD is altered, abortive DNA products are observed during leading strand synthesis. Loop B appears to play an important role in communication with the helicase and gp2.5, whereas loop A plays a stabilizing role in these interactions.

Base Pair-Position-Specific DNA ‘Breathing’ At the Replication Fork Junction Regulates Helicase Access

Thermal fluctuations induce transient opening of base pairs in dsDNA constructs. In previous studies with DNA constructs of conserved sequence containing 2-AminoPurine (2-AP) probes, we showed that position-specific base-pair (bp) fraying that depends on proximity to the ss/ds junction can be observed in forked DNA constructs of conserved sequence, and that significant (>1%) thermal fraying of base-pairs at helix ends extends 2-3 bps into the dsDNA. Here we build on these results to study the initial steps of DNA helicases at replication forks. Proteins that bind preferentially to ssDNA can capture thermally frayed bps without the expenditure of chemical (NTP-dependent) free energy. The bacteriophage T4 DNA replication complex provides a favorable model system to study basic helicase mechanisms. The T4 helicase-primase (gp41-gp61) sub-assembly forms a tight-binding helicase that unwinds dsDNA and translocates processively along ssDNA lattices, driven by NTP binding and hydrolysis. We use fluorescence and low energy CD spectral signals of site-specifically placed 2-AP probes to monitor the initial steps of helicase activity at a forked DNA construct. We find, on binding a helicase-primase complex to the DNA construct in the presence of non-hydrolysable NTP, that the first bp on the duplex side of the fork opens and additional destabilization penetrates to ∼ the 3rd bp. This is consistent with a largely passive mechanism for helicase-dependent DNA unwinding, with the helicase complex binding on the 5′→3′ loading strand at the fork and trapping the first adjacent bp as it is opened by thermal fluctuations.

Structure–Function Defects of the TWINKLE Linker Region in Progressive External Ophthalmoplegia

TWINKLE is the helicase at the mitochondrial DNA (mtDNA) replication fork in mammalian cells. Mutations in the PEO1 gene, which encodes TWINKLE, cause autosomal dominant progressive external ophthalmoplegia (AdPEO), a disorder associated with deletions in mtDNA. Here, we characterized seven different AdPEO-causing mutations in the linker region of TWINKLE and we identified distinct molecular phenotypes. For some mutations, protein hexamerization and DNA helicase activity are completely abolished whereas others display more subtle effects. To better understand these distinct phenotypes, we constructed a molecular model of TWINKLE based on the three-dimensional structure of the bacteriophage T7 gene 4 protein. The structural model explains the molecular phenotypes and also predicts the functional consequences of other AdPEO-causing mutations. Our findings provide a molecular platform for further studies in cell- and animal-based model systems and demonstrate that knowledge of the bacteriophage T7 DNA replication machinery may be key to understanding the molecular and phenotypic consequences of mutations in the mtDNA replication apparatus.

The Control Mechanism for Lagging Strand Polymerase Recycling during Bacteriophage T4 DNA Replication

Given the polarity of DNA duplex, replication by the leading strand polymerase is continuous whereas that by the lagging strand polymerase is discontinuous proceeding through Okazaki fragments. Yet the respective polymerases act processively, implying that the recycling of the lagging strand polymerase is a controlled process. We demonstrate that the rate of the lagging strand polymerase relative to that of fork movement affects Okazaki fragment size and generates ssDNA gaps. We show by using a substrate with limited priming sites that Okazaki fragments can be shifted to shorter lengths by varying the rate of the primase. We find that clamp and clamp loader levels affect both primer utilization and Okazaki fragment size, possibly implicating clamp loading onto the RNA primer in the mechanism of lagging strand polymerase recycling. We formulate a signaling model capable of rationalizing the distribution of Okazaki fragments under various conditions for this and possibly other replisomes.

Interaction between the T4 Helicase Loading Protein (gp59) and the DNA Polymerase (gp43): Unlocking of the gp59−gp43−DNA Complex to Initiate Assembly of A Fully Functional Replisome

Single-molecule fluorescence resonance energy transfer and functional assays have been used to study the initiation and regulation of the bacteriophage T4 DNA replication system. Previous work has demonstrated that a complex of the helicase loading protein (gp59) and the DNA polymerase (gp43) on forked DNA totally inhibits the polymerase and exonuclease activities of gp43 by a molecular locking mechanism (Xi, J., Zhuang, Z., Zhang, Z., Selzer, T., Spiering, M. M., Hammes, G. G., and Benkovic, S. J. (2005) Biochemistry 44, 2305-2318). We now show that this complex is "unlocked" by the addition of the helicase (gp41) with restoration of the DNA polymerase activity. Gp59 retains its ability to load the helicase while forming a gp59-gp43 complex at a DNA fork in the presence of the single-stranded DNA binding protein (gp32). Upon the addition of gp41 and MgATP, gp59 dissociates from the complex, and the DNA-bound gp41 is capable of recruiting the primase (gp61) to form a functional primosome and, subsequently, a fully active replisome. Functional assays of leading- and lagging-strand synthesis on an active replication fork show that the absence of gp59 has no effect on the coupling of leading- and lagging-strand synthesis or on the size of the Okazaki DNA fragments. We conclude that gp59 acts in a manner similar to the clamp loader to ensure proper assembly of the replisome and does not remain as a replisome component during active replication.

Maturation of Bacteriophage T4 Lagging Strand Fragments Depends on Interaction of T4 RNase H with T4 32 Protein Rather than the T4 Gene 45 Clamp

In the bacteriophage T4 DNA replication system, T4 RNase H removes the RNA primers and some adjacent DNA before the lagging strand fragments are ligated. This 5'-nuclease has strong structural and functional similarity to the FEN1 nuclease family. We have shown previously that T4 32 protein binds DNA behind the nuclease and increases its processivity. Here we show that T4 RNase H with a C-terminal deletion (residues 278-305) retains its exonuclease activity but is no longer affected by 32 protein. T4 gene 45 replication clamp stimulates T4 RNase H on nicked or gapped substrates, where it can be loaded behind the nuclease, but does not increase its processivity. An N-terminal deletion (residues 2-10) of a conserved clamp interaction motif eliminates stimulation by the clamp. In the crystal structure of T4 RNase H, the binding sites for the clamp at the N terminus and for 32 protein at the C terminus are located close together, away from the catalytic site of the enzyme. By using mutant T4 RNase H with deletions in the binding site for either the clamp or 32 protein, we show that it is the interaction of T4 RNase H with 32 protein, rather than the clamp, that most affects the maturation of lagging strand fragments in the T4 replication system in vitro and T4 phage production in vivo.