Processive Replication of Single-stranded DNA Templates by the ...

THEJOURNAL OF BIOLOGICAL CHEMISTRY

Vol. 262, No. 9, Issue of March 25, pp. 4252-4259,1987 Printed in U.S.A.

0 1987 by The American Society of Biological Chemists, Inc.

Processive Replication of Single-stranded DNA Templates by the Herpes Simplex Virus-induced DNA Polymerase* (Received for publication, September 22, 1986)

Michael E.O’DonnellS, Per Eliass, and I. R. Lehman From the Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305

The DNA polymerase encoded by herpes simplex virus 1 consists of a single polypeptide of M, 136,000 that has both DNA polymerase and 3’+5’ exonuclease activities; it lacks a 5‘+3‘ exonuclease. The herpes polymerase is exceptionally slow in extending a synthetic DNA primer annealed to circular singlestranded DNA (turnover number -0.25 nucleotide). Nevertheless, it is highly processive because of its extremely tight binding to a primer terminus (& e 1 nM). The single-stranded DNA-binding protein from Escherichia coli greatly stimulates the rate (turnover number -4.5 nucleotides) by facilitating the efficient binding to and extension of the DNA primers. Synchronous replication by the polymerase of primed single-stranded DNA circles coated withthesinglestranded DNA-binding protein proceeds to the last nucleotide of available 5.4-kilobase template without dissociation, despite the 20-30 min required to replicate the circle. Upon completion of synthesis, the polymerase is slow in cycling to other primed single-stranded DNA circles. ATP (or dATP) is not required to initiate or sustain highly processive synthesis. The 3‘+5‘ exonuclease associated with the herpesDNA polymerase binds a 3’ terminus tightly ( K , < 50 nM) and is as sensitive as the polymerase activity to inhibition by phosphonoacetic acid (Ki -4 h ~ )suggesting , closecommunication between the polymerase and exonuclease sites.

a single-stranded DNA-binding protein (2). Partial purification of the herpes DNA polymerase has shown it to be a n approximately150-kDa polypeptide (3) in good agreement withthe molecularmass of 136 kDapredicted from the nucleotide sequence of the gene (4, 5). As a first step in our analysis of HSV-1 DNAreplication, we havepurified the herpes-induced DNA polymerase to homogeneity and examined the dynamicsof its replication of ssDNA templates. A second viral encoded protein known to be essential for HSV-1 DNA replication, ICP8 (6-8), binds ssDNA tightly and cooperatively (9) and is therefore analogous to the prokaryotic single-stranded DNA-binding proteins typified by Escherichia coli SSB and T 4 gene 32 protein (1).The interaction of ICP8 with the DNA polymerase in the presence of single- and double-strandedDNA templates is the subject of the accompanying paper (10). EXPERIMENTALPROCEDURES

Materials-Unlabeled and labeled nucleotides were purchased from PharmaciaP-L Biochemicals and Amersham Corp., respectively. dAMP-PNP was a gift from Dr. B. Alberts (University of California, San Francisco). $X and Ml3Goril viral DNAs were prepared as described (11); all viral DNA concentrations are expressed as DNA molecules and were calculated using an AZWof 1 as equivalent to 36 pg/ml. (dA)lmand (dT)17 were purchased from Pharmacia P-L Biochemicals. Calf thymus DNA, purchased from Sigma, was activated as described (12). SSB (4 X lo4 units/mg) (13) was a gift from Dr. D. Soltis (this department). DNA polymerase 111 holoenzyme fraction V (7 X lo6 units/mg) was prepared as described (14). E. coli DNA ligase was prepared as described (15). T4 DNA polymerase and The replication of a duplex DNA chromosomerequires the T 4 polynucleotide kinase were obtained from the United States Biochemical Co. Phosphonoacetic acid was obtained from Sigma. concerted actionof several proteins that are thought to assemBio-Gel A-1.5m and proteinmolecular weight markers were obtained ble into a multiprotein complex (1).T o understand the mo- from Bio-Rad.Plastic-backed polyethyleneimine-cellulose sheets lecular mechanism bywhich a eukaryotic chromosome is (Polygram MN300) were obtained from BrinkmannInstruments; replicated, we have chosen to study herpes simplex virus 1 Centricon 10 was from Amicon. Bufiers-Buffer A was 20 mM Tris-C1 (pH 7.5), 6 mM MgClz, 4% (HSV-l).’ The HSV-1 genome which is a linear duplex apmM proximately 150 kb in length encodes many of the enzymes glycerol, 0.1 mM EDTA, 40 pg/ml bovine serumalbumin,5 required for its replication, including a DNA polymerase and dithiothreitol. Buffer B was 20 mM Hepes/Na+ (pH 7.5), 0.5 mM dithiothreitol, 0.5 mM EDTA, 0.5 mM phenylmethylsulfonyl fluoride, * This research was supported by Grant GM06196 from the Na- 10% (w/v) glycerol. Buffer C was 50 mM Tris-C1 (pH 7.5), 150 mM tional Institutes of Health. The costs of publication of this article (NH,),SO,, 0.5 mM dithiothreitol, 0.1 mM EDTA. Cells and Viruses”RA305 (16), a thymidine kinase-deficient muwere defrayed in part by the payment of page charges. This article must therefore be hereby marked “advertisement” in accordance with tant of HSV-1 [F], was used to infect roller-bottle cultures of Vero cells using a multiplicity of infection of 5-10 plaque-forming units/ 18 U.S.C. Section 1734 solely to indicate this fact. $ Fellow of the Helen Hay Whitney Foundation. Present address: cell. Purification of HSV-1 DNA Polymeruse-The herpes-induced Dept. of Microbiology, Cornel1 University Medical School, 1300 York DNA polymerase was purified by a modification of the method of Ave., New York, NY 10021. 5 Supported by a fellowship from the Knut and Alice Wallenberg Powell and Purifoy (3). The steps in thepurification up to chromatography onphosphocellulose have been described (17). Briefly, nuclei Foundation, Sweden. The abbreviations used are: HSV, herpes simplex virus; Hepes, were prepared from 50 roller bottles of infected cells (32 g, wet weight) 4-(2-hydroxyethyl)-l-piperazineethanesulfonic acid; dNTPs, deoxy- and extracted with 1.7 M NaC1. The DNA was removed by ultracenribonucleoside triphosphates; MMP-PNP, 2’-deoxy-5’-adenyl imi- trifugation at 100,000 X g, and the supernatant(200 ml) was dialyzed dodiphosphate; $X, bacteriophage 4x174; ssDNA, single-stranded for 6 h against two changes (2 liters each) of buffer B and loaded DNA; RFI, closed circular duplex DNA; RF 11, circular duplex DNA onto a phosphocellulose column (16-ml bed volume) equilibrated with with a nick in one strand; kb, kilobases; SDS, sodium dodecyl sulfate; buffer B. The phosphocellulose column was eluted with alinear SSB, E. coli single-stranded DNA-binding protein; ICP8, infected cell gradient from 0.1 to 0.6 M NaCl in a total volume of 200 ml of buffer B. Herpes DNA polymerase activity eluted at approximately 0.3 M protein 8.

’

4252

4253

HSV-1 DNA Polymerase TABLE I Purification of HSV-1 DNA polymerase from HSV-1-infected Vero rdls

Fraction

Total

Total

protein activitf units x mg

10"

Specific activity unitslmg x 10-6

Overall Purifiyield cation

7%

-fold

Ia. Cytoplasm 1.9 267 0.79 12 Ib. Nuclear extract Before dialysis 123 13.0 10.5 82 After dialysis 60 14.0 23 88 6b 4.8 61 30 16 11. Phosphocellulose 7.9 23 326 111. DNA-cellulose 0.30 3.7 1230 0.12 2.6 2200 16 583 IV. Glycerol gradient One unit is eaual to 1 pmol of DNA synthesis in 10 min at 37 "C. Relative to the combined fractions Ia and Ib(before dialysis). NaC1. Polymerase fractions were pooled, dialyzed, and applied to a 5-ml ssDNA-cellulose column (prepared as described in Ref. 18) equilibrated withbuffer B containing 30% (w/v) glycerol. The column was eluted with a linear gradient from 0.1 to 1.0 M NaCl in a total volume of 100 ml of buffer B containing 30% (w/v) glycerol. DNA polymerase eluted at approximately 0.3 M NaCl. Active fractions were pooled, dialyzed against buffer C containing 5% (w/v) glycerol, and concentrated by ultrafiltration in a centrifuge (Centricon 10) to 0.75 mg/ml in a total volume of 400 pl.The concentratedDNA polymerase fraction was divided into two equal portions, and each was loaded onto a 10.6-ml linear 10-30% gradient of glycerol in buffer C. The glycerol gradients were centrifuged a t 40,000 rpm in aBeckman SW41.Ti rotor for 40 h at 4 "C. After centrifugation, 0.2-ml fractions were collected from the bottom of the tubes. The purificationis summarized in Table I. Fractions at each step of purification were also analyzed by electrophoresis in a 7.5% SDS-polyacrylamide gel, and proteins were visualized by staining with Coomassie Blue (19). Protein concentration was measured by a modification of the method of Bradford (see Ref. 20) using bovine serum albumin as a reference. The concentration of active DNA polymerase molecules was determined from the amount of SSB-coated singly primed circular @X ssDNA that was replicated by a given amount of polymerase in 40 min at 30 "C (assuming one polymerase molecule/primer terminus). The number of circles replicated was calculated from the total amount of DNA synthesis, the specific activity of nucleotides, and the size of the primed ssDNA circle (21) (i.e. moles of nucleotide polymerized per 5386). Templates-The sequence and synthesis of the deoxyoligonucleotide 15-mer primers are described in a previous report (22). In most of these studies, the @X ssDNA was primed with primer 1; in one experiment, the ssDNA was primed with primer 4 (see text). The M13Goril ssDNA was primed using primer 5. Hybridization of synthetic primers (2.1 p~ 15-mer) to viral ssDNA (160 nM circles) was in 10 mM Tris-C1, 0.3 M NaCl, and 0.03 M sodium citrate (final pH 8.5). The hydridization mixture was heated briefly to 100 "C, allowed to cool to room temperature over 20 min, and incubated a further 1 h at 30 "C. Primed @X ssDNA labeled at the 5' terminus of the synthetic DNA primer was made by labeling the primer with T4 polynucleotide kinase and [ T - ~ ~ P I A Tand P , then hybridizing the labeled primer to @XssDNA, followed by filtration on Bio-Gel A-1.5m in 10 mM TrisC1 (pH 7.5), 0.5 mM EDTA, 100 mM NaCl to remove excess labeled ATP and primer. (dA)1000.(dT)17 was made by incubating (dA)lwo (0.5 mg/ml) and (dT),, (5 pg/ml) in 10 mM Tris-HC1, 0.3 M NaC1, and 0.03 M sodium citrate (final pH 8.5) at 30 "C for 1 h. Synthetic 3'end-labeled hairpin templates (synthetic 57-mers) with either a paired 3'-deoxyadenylate or unpaired 3"deoxythyrnidylate were generously provided by Hisaji Maki (thisdepartment).' Measurement of DNA Synthesis-For the assay of DNA polymerase activity during purification, reaction mixtures (25 pl) contained 2.2 pg of activated DNA, 0.5 mM ATP, 60 p~ each dATP, dCTP, and dGTP, 5 p M [3H]dTTP (40 Ci/mmol), and 150 mM (NH,),SO, in buffer A contalnlng 3 mM MgCl,. The reaction was initiated by adding 1 pl of enzyme fraction containing up to 30 units of DNA polymerase. Incubation was for 10 min at 37 "C. Reactions were quenched with 1 ml of cold 10% trichloroacetic acid, 0.1 M pyrophos-

H. Maki and A. Kornberg, manuscript in preparation.

phate. Incorporation of labeled nucleotide into acid-insoluble material was measured as described (22). Specific details of DNA synthesis on singly primed @XssDNA are given in the figure legends. Reactions were incubated at 30 "C, and samples taken at the timesindicated were quenched by adding them to an equal volume of 1%SDS, 40 mM EDTA. The samples, after quenching, were usually divided into two parts. One-half was analyzed for DNA synthesis by measuring the total nucleotide incorporated into acid-insoluble material as described (22). (The values for DNA synthesis refer to the entire reaction mixture). The other half was used for the analysis of the replication products by electrophoresis in neutral 0.8% agarose gels as described (22).Forautoradiography, dried gels were exposed to Kodak XAR-5 x-ray film. Measurement of3"Hj' Exonuclease Actiuity-Synthetic DNA hairpin templates containing either paired or unpaired 3"labeled termini were used as substratesfor measurement of 3'+5' exonuclease activity. Reaction mixtures (12.5 pl) contained 3.1 pmol of hairpin template, 83 fmol of DNA polymerase, and 60 mM NaCl in buffer A. When present, dNTPs were 60 p~ each. Incubation was at 30 "C. Samples (1 pl) were quenched instantly upon being spotted onto polyethyleneimine-cellulose strips containing ATP and ADP as carrier and developed in 1 M formic acid and 0.5 M LiCl. Positions of unused substrate (origin) and dTMP or dAMP (near the solvent front) were identified by autoradiography andcut out, andtheir radioactivity was determined by scintillation counting. RESULTS

HSV-1 DNA Polymerase Is Stimulated by E. coli SSBThe HSV-1 DNA polymerase was only minimally active with circular 4X ssDNA (5.4 kb) primed with a synthetic 15-mer (Fig. 1).Activity was, however, stimulated more than 20-fold upon coating the primed ssDNA with E. coli SSB (Fig. 1). The herpesDNA polymerase was also stimulated (1.5-5-fold) by 250 mM NaCl (data not shown), the extentof stimulation depending upon the relative amounts of DNA polymerase and DNA in the assay. The influence of ionic strength onpolymerase activity when the herpes DNA polymerase was in molar excess over singly primed ssDNA circles is shown in Fig. 2. DNA polymerase activity was stimulated %fold by 150 mM NaCl at early times

10

20

30

40

50

60

MINUTES

FIG. 1. Stimulation of HSV-1 DNA polymerase by E. coli SSB. Herpes DNA polymerase (13 fmol) was incubated with 78 ng of singly primed 4X ssDNA (45 fmol as circles) in buffer A (168 pl) containing 60 p~ each dCTP and dGTP. The reaction mixture was incubated 3 min and then replication was initiated by addition of 7 plof1.5 mM dATP and 0.5 mM [a-32P]d'M'P (2400 cpm/pmol). Samples (20 pl) were removed a t the times indicated, quenched, and analyzed for DNA synthesis as described under "Experimental Procedures." A, no additions; 0, ssDNA was coated with 0.78 pg of SSB.

HSV-1 DNA Polymerase

4254

of SSB, theherpes DNA polymerase was maximally active on SSB-coated ssDNA at anionic strength of approximately 70 mM (data notshown). HSV-1 DNA Polymerase Is Highly Processiue-DNA synthesis by the herpes DNA polymerase withSSB-coated 25 ssDNA as template reached a plateau value after 20-30 min even though all of the available DNA had notbeen replicated -(Fig. 1). Moreover, the extent of DNA synthesis was proportional to the amount of DNA polymerase added (data not - 20 II shown). The limited DNA synthesis suggests a highly procesY sive mode of nucleotide polymerization wherein each polymX erase molecule completely extends a DNA primer around the 5> 15 ssDNA circle without dissociation and is slow in cycling to a another primed template. z n Analysis of replication products from singly primed SSB10 coated ssDNA by native agarose gel electrophoresis supports the highly processive mode of nucleotide polymerization (Fig. 3B). During the time in which full-length products (RF 11) 5 were formed, most of the primed ssDNA remained unchanged (detected by UV-induced ethidium bromide fluorescence). The 20 min required for the complete replication of a 4X ssDNA molecule (5.4 kb) yields an average turnover number 15 10 5 of 4.5 nucleotides/s/polymerase molecule. The lack of signifMINUTES icant radioactivity in theregion of the gel between the primed FIG. 2. Influence of ionic strength on replication of singly ssDNA and RFI1 product after 30 min indicates that cycling primed &X ssDNA. Reaction mixtures (125 pl) contained 204 fmol of singly primed @XssDNA (as circles), 500 fmol of herpes DNA of the polymerase to otherprimed ssDNA molecules is slow. polymerase, 0.5 mM ATP, 60 p~ dCTP, dGTP, and dATP, and 20 That the remaining primed circles were effective templates was demonstrated by their replication upon further addition p~ [m3*P]dTTP(3000 cpm/pmol) in buffer A. Samples (20 pl) were removed at the indicated times, quenched, and analyzed for DNA of DNA polymerase (not shown). synthesis as described under “Experimental Procedures.” The conThe herpes DNA polymerase was also highly processive in centration of NaCl in individual reactions was: A, 0; 0 , 3 0 mM; A, 60 the absence of SSB. An agarose gel analysis of the replication mM; 0,90 mM; 0, 120 mM; 0 , 1 5 0 mM. products formed with singly primed 4X ssDNA showed that A ) NO ADDITION B) SSB ADDED most of the DNA templates had not reacted; nevertheless, discrete, partially replicated species and some fully replicated MIN: 10 2 0 40 60 MIN: 3 6 10 2 0 30 RF I1 molecules were evident (Fig. 3A). The processivity of the HSV-1 DNA polymerase was demcRFll a-RFII onstrated in a second type of experiment diagramed in Fig. 4A. The DNA polymerase was preincubated with an 18-fold excess of singly primed +X ssDNA coated with SSB so that each polymerase molecule was bound to a primer terminus. dCTP and dGTP (the 3”terminal nucleotides of the primer and the first4 nucleotides needed for synthesis) were present during the preincubation to protect theprimer from removal of the terminalnucleotides by the 3‘+5‘ exonuclease activity of the polymerase (see below). After a short preincubation -%DNA period, an excess (%fold over 4X ssDNA circles) of challenge cssDNA DNA, i.e. singly primed,M13Goril ssDNA (8.6 kb), was FIG. 3. Time course of replication of singlyprimed &X added. After further preincubation for either 5 s or 3 min, ssDNA analyzed by neutral agarose gel electrophoresis. Au- replication was initiated by the addition of dATP and[ c Y - ~ ~ P ] toradiogramsof 0.8%neutral agarose gel electrophoresis of replication dTTP; after6 min, further incorporation of radioactivity was reactions of Fig. 1in the absence of SSB ( A )and replication reactions prevented by addition of excess unlabeled dTTP. Incubation of Fig. 1 in the presence of SSB (B). Electrophoresis and autoradiog- for an additional 40 min ensured complete replication of raphy were as described under “Experimental Procedures.” The arrows mark the ,position of RF I1 DNA and singly primed ssDNA templates towhich a polymerase molecule was bound at the time unlabeled dTTP was added. Analysis of the replication standards detected by UV-induced ethidium bromide fluorescence. products by agarose gel electrophoresis is shown is Fig. 4B. in the reaction (2-3 min). However, at later times (after 5 Essentially allthe label was incorporated into the4X ssDNA min), thepolymerase activity was maximal at 60-90 mM NaCl template following the 5-s preincubation period. Hence, the and then decreased progressively as the salt concentration herpes DNA polymerase remained bound to the 4X DNA was increased. Analysis of the products of replication by during synthesis.After a 3-min preincubation period, most of neutral agarose gel electrophoresis showed that most of the the radioactivity was associated with the 4X DNA, showing only minimal transfer of the herpes polymerase to the chalprimers were extended to a few uniquepositions on the circular template (data notshown, but see Fig. 3A). A differ- lenging M13Goril DNA before initiation of synthesis.A ent setof polymerase pause or termination sites was observed controlreaction in which the polymerase was added to a with another 15-mer (primer 4 in Ref. 22) which hybridizes mixture of $X and M13GorilssDNAs showed about twice as to 4X ssDNA at a site 1.9 kb distant from the primer 1 15- much incorporation of labeled nucleotide into the M13Goril $X ssDNA (Fig. 4B, third l a n e ) , consistent mer. In contrast to thestimulation of activity in the absence ssDNA as into the I

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FIG.4. Processive DNA replication by herpes DNA polymerase in presenceof challengingtemplate. A , scheme of challenge experiment. Herpes DNA polymerase (7 fmol) was preincubated for 3 min (30 "C) with 120 fmol of singly primed 4X ssDNA (as circles) coated with SSB (2.2 pg) in 25 p1 of buffer A containing 60 p~ each dCTP and dGTP.After the preincubation, the reaction was mixed with a solution (25 pl) containing 240 fmol of singly primed M13Goril ssDNA (as circles) and 6.9 pg of SSB in buffer A containing60 p~ each dGTP anddCTP. After further incubation for either 5 s or 3 min, 2 pl of a solution containing 1.5 mM dATP and 0.5 mM [m3*P] dTTP (3725 cpm/pmol) was added. After 6 min, excess unlabeled dTTP was added (1 mM final concentration), and the incubation was continued for 40 min before quenching with an equal volume of 1%SDS and 40 mM EDTA. B, autoradiogram of 0.8% neutral agarose gel electrophoresis of replication reactions. Addition of dATP and [ c Y - ~ ~ P I ~was T T Peither 5 s (first lune) or 3 min (second l a n e ) after addition of Ml3Goril DNA. The third lune (marked C ) is a control reaction where herpes DNA polymerase was added to a mixture of the @X(120 fmol) and Ml3Goril (240 fmol) ssDNAs. The tick marks correspond to theposition of DNA standards detected by UVinduced ethidium bromide fluorescence. with the molar excess of M13Goril over 4X ssDNA circles. The concentrations of primed DNA circles and HSV-1 DNA polymerase in the experiments of Figs. 3 and 4 provide an upper limit of 1 nM for the equilibrium dissociation constant (&) for polymerase binding to a primer-template. Unlike E. coli DNA polymerase I11 holoenzyme, whose tight binding to DNA and highly processive DNA synthesis requires ATP (or dATP) hydrolysis, there was no effect of ATP or dAMP-PNP on processive DNA synthesis by the HSV-1 DNA polymerase (data notshown). HSV-1 DNA Polymerase Completely Replicates Primed 4X ssDNA Circles-To determine the extent to which the circular DNA template is replicated by the herpes DNA polymerase, the products of replication of singly primed 4X ssDNA were treated with E. coli DNA ligase, which requires directly apposing 3'-hydroxyl and 5'-phosphoryl termini toform a phosphodiester bond (23). In the experiment shown in Fig. 5, a portion of the reaction mixture was removed after 10 min, and E. coli DNA ligase and NAD+ were added. Samples were removed after an additional 10, 20, and 30 min of incubation and analyzed by electrophoresis in an agarose gel containing ethidium bromide (Fig. 5B, eighth to tenth lanes). Approximately 70% of the RFI1 products of polymerase action were sealed by the DNA ligase within 30 min and asa consequence co-migrated with a closed circular duplex DNA marker. It therefore appears that synthesis by the herpes DNA polymerase proceeds directly to the 5' terminus of the primer, leaving a nick that canbe sealed by DNA ligase. HSV-1 DNA Polymerase Lacks 5 ' 4 ' Exonuclease Activity-The experiment used to test for 5'+3' exonuclease activity associated with the herpes DNA polymerase is diagramed in Fig. 5A. A 2-fold molar excess of polymerase was added to SSB-coated 4X ssDNA primed with a synthetic 15mer labeled with 32Pa t its 5' terminus. Samplesof the reaction were removed a t intervals up to 30 min, the time required to

replicate the entire circular template. If the polymerase has significant 5'43' exonuclease activity, it should remove the 32P-labeled 5"terminal nucleotide of the primer upon complete replication of the template. As shown in Fig. 5B, the 5'terminal nucleotide persisted throughout the 30-min period of replication. Quantitation of radioactivity of excised gel slices showed that after30 min, the 32Pat theposition of the completed RF I1 circles was approximately 75% that of the primer before the beginning of replication (0 min); 19%of the remaining 32Pwas present in the smear below the RF I1 products. The reaction of Fig. 5 was initiated by adding DNA polymerase to a solution containing the primed DNA and all four dNTPs; hence, the replication intermediates appeared as a smear. A discreteband of replication intermediates (as inFig. 3) is observed only when the polymerase is preincubated for a brief period with the primed DNA and synchronous replication is initiated by addition of the dNTPs. Herpes DNA Polymerase and 3 ' 4 ' Exonuclease Are Present within the Same Polypeptide-The HSV-1 DNA polymerase and its associated 3'45' exonuclease co-sediment perfectly in a 10-30% glycerol gradient at theposition of a 158kDa marker protein (Fig. 6A), consistent with previous reports (24, 25). Moreover, as shown in Fig. 6B, the herpes DNA polymerase is nearly homogeneous (>go%) as judged by Coomassie Blue staining of the gradient fractions following SDS-polyacrylamide gel electrophoresis. The DNA polymerase and 3'+5' exonuclease active sites would therefore appear to reside within the same polypeptide chain. The herpes polymerase showed no detectable primase activity (data not shown). 3 ' 4 ' Exonuclease Has Proofreading Activity-An earlier report demonstrated that the 3'+5' exonuclease associated with the herpes DNA polymerase has proofreading activity (26). We have examined the proofreading capacity of the 3'+

HSV-1 DNA Polymerase

4256 A)

5’ LABELLED DNA 15-MER

V

RFIl

DNA LIGASE

RFI

* B)

MINUTES: 0

3 6 10 15 2030 10 20 30 =-RFlI

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(Table 11)is considered more fully in the accompanying report (10). During DNA synthesis with the homopolymer template, (dA)looo. (dT),,, a significantamount of dTMP was generated, approximately 10% of the level incorporated into the homopolymer (compare Fig. 7, B and C). However, in the absence of aprimer-template, dTMP was not produced (data not shown). The dTMPis most likely formed upon hydrolysis of paired 3’ termini during DNA synthesis as observed previously for the herpes polymerase (25) and for other DNA polymerases that contain3‘+5‘ exonuclease activity (1). Phosphonoacetic Acid Inhibits DNA Polymerase and 3 ‘ 4 ’ Exonuclease to Equal Extents duringDNA Synthesis-Phosphonoacetic acid inhibits both the polymerase and 3’+5’ exonuclease activities of the herpes DNA polymerase with a K j value of approximately 4 p M (Fig. 8, A and B ) . In the absence of dNTPs, theKi for phosphonoacetic acid inhibition of the 3’+5’ exonuclease on the hairpin template with either paired or unpaired 3’ termini is 50 p~ (Table 11), the same as the K , for hydrolysis of both paired and unpaired 3’-terminal nucleotides (see above). DISCUSSION

Despite its slow rate of DNA synthesis, the HSV-1-induced +ssDNA DNA polymerase is strikingly processive. Once bound to its primer-template, the herpes polymerase does not dissociate FIG.5. Complete replication of primed &X ssDNA circles by herpes DNA polymerase which lacks 5‘43’ exonuclease ac- during the approximately 20 min required to fully replicate a tivity. A , scheme for detecting 5’+3’ exonuclease activity activity 5.4-kb +X ssDNA circle. This highly processive mode of and complete replication of ssDNA. The 5’ end-labeled 15-mer primer nucleotide polymerization may be ofimportance in replicating annealed to @XssDNA was prepared as described under “Experimen- the 150-kb viral chromosome and, even more important, in tal Procedures.” A slight excess of herpes DNA polymerase (1000 the synthesis of multiple copies of the genome in rolling circle fmol) was added to initiate replication of the singly primed @XssDNA DNA replication (2). Although it is not known whether Oka(1.3 pg, 750 fmol as circles) in 150 pl of buffer A containing 13 pg of SSB, 0.5 mM ATP, 60 p~ dCTP, dGTP, and dATP, and20 p~ [3H] zaki fragments are intermediates in replication of the herpes removed and chromosome, the high processivity, replication to a nick sealdTTP (2500 cpm/pmol). After 10 min, 50plwas incubated with NAD+ (0.1 mM final concentration) and 0.3 pg of E. able by DNA ligase, and lack of 5‘+3‘ exonuclease activity coli DNA ligase.Samples (12.5 pl) were removed at thetimes indicated are clearly desirable features in thesynthesis of discontinuous and quenched with SDS/EDTA; the DNA products were analyzed by DNA fragments. neutral agarose gel electrophoresis; and DNA synthesis was quantiThe rateof fork movement during replication of pseudoratated as described under “Experimental Procedures.” €?,autoradibies virus, a member of the herpes virus family, is approxiogram of 0.8% neutral agarose gel electrophoresis of the products of replication. Eight to tenth lunes, the time noted is after the addition mately 50 nucleotides/s at 37 “C (26),similar to that of of ligase. Arrows mark the positions of RF 11, RF I, and ssDNA eukaryotic chromosomes (27, 28). One might therefore anticstandards detected by UV-induced ethidium bromide (EtBr)fluores- ipate a turnover number of at least 30-40 nucleotides/s for cence. the herpes DNA polymerase at 30 “C. The apparentturnover number of 0.25 nucleotide/s with singly primed 4X ssDNa 5’ exonuclease using defined synthetic DNA hairpin tem- circles is far too low to sustainproductive herpes virus infecplates (57-mers) having either a paired or unpaired labeled 3‘ tion (assuming 10,000 copies/cell in 10 h). However, the 20terminus (diagramed in Fig. 7A). In the presence of the 4 fold stimulation of the herpes DNA polymerase upon coating dNTPs, the 3‘+5‘ exonuclease completely removed the un- the ssDNA with E. coli SSB approaches the ratein uiuo. HSV1 may therefore encode a functional analogue of E. coli SSB. paired3‘-terminal nucleotide (Fig. 7B).Incontrast,the Like E. coli SSB, the herpes-induced ICP8 binds tightly and paired 3‘ terminus was stable to the 3‘45’exonuclease in the presence of dNTPs (Fig. 7B), due presumably to theaddition cooperatively to ssDNA (9), is essential for ongoing DNA of nucleotides to the paired 3‘ terminus by the polymerase. replication (8), and is present a t stoichiometric levels (29). However, despite its similarity to the E. coli SSB, binding of The 3’+5’ exonuclease hydrolyzed an unpaired 3’-terminal nucleotide at justover twice the rate atwhich the paired 3’- ICP8 to ssDNA completely inhibits the replication of singly terminal nucleotide was hydrolyzed (Fig. 7C). The rates of primed +X ssDNA by herpes DNA polymerase (10). In conhydrolysis of paired and unpaired 3‘-terminal nucleotides did trast, ICP8markedly stimulates synthesis by the polymerase not change over the range 1p M to 50 nM template, setting an on duplex DNA templates (10). E. coli DNA polymerase I11 holoenzyme hydrolyzes the P,rupper limit of the K , for hydrolysis at 50 nM (Table 11). Since substrate was present at saturating concentrations, apparent phosphodiester bond of ATP (or dATP) to initiate highly turnover numbers for removal of paired and unpaired 3’- processive DNA synthesis (22). In contrast, the monomeric terminal nucleotides could be calculated from the observed herpes DNA polymerase does not require ATP or dATP. hydrolysis of the rates of hydrolysis (Table 11). Use of Mn2+ inplace of Mg2+ Thus, a complex subunitstructureand hadno effect on the rate of hydrolysis of the paired 3’ terminal phosphate of ATP or dATP are not essential for terminus but stimulatedremoval of the unpaired 3’ terminus highly processive DNA synthesis. The response of the herpes DNA polymerase to ionic 1.5-fold (Table 11). The effect of the herpes-encoded ssDNAbinding protein,ICP8,on the 3‘+5‘ exonuclease activity strength is complex. At a molar excess of DNA polymerase to

HSV-1 DNA Polvmerase

4257 B)

-

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FIG. 6. Glycerol gradient sedimentation analysis of herpes DNA polymerase. A, glycerol gradient sedimentation of herpes DNA polymerase is described under“Experimental Procedures.” DNA polymerase (Pol, 0) was assayed using activated calf thymus DNA, and the 3’+5’ exonuclease (Exo, A) was assayed using the synthetic 57mer hairpin DNA with a labeled unpaired 3’ terminus as described under “Experimental Procedures.” Position of protein standards in a parallel glycerol gradient are marked by brackets. B, SDSpolyacrylamide gel electrophoresis of glycerol gradient peak fractions. The tick marks correspond tothe migration of molecular mass standards in the same gel. 40

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10

FRACTION NUMBER

TABLE I1 Steady state kinetic parameters for hydrolysis of pairedand unpaired 3’ termini by 3‘+5‘ exonuclease of HSV-1 DNA polymerase 3‘ termini

AI 3’PAIRED 7 21

A 18

3’ UNPAIRED

Unpaired Paired

* 22

Turnover number (nucleotides/s) 30 “C, no addition 0.16 0.066 37 “C, no addition 0.23 0.073 30 “C, ICP8 added 0.046 0.178 30 “C, Mn2+ 0.066 K , 3’ termini ( p ~ ) C0.05 5000 Processivity J. Virol. 37, 191-206 Inhibits Stimulates Effect of 0.2 M NaC1’ 7. Weller, S. K., Lee, K. J., Sabourin, D. J., and Shaffer, P. A. Inhibition by PAAd No Yes (1983) J. Virol. 45, 354-366 DNA polymerase from Drosophila embryos (33). 8. Shaffer, P. A., Bone, D. R., and Courtney, R. J. (1976) J. Virol. * Singly primed 4X ssDNA coated with E. coli SSB astemplate. 17,1043-1048 e Activated calf thymus DNA template. 9. Ruyechan, W. T. (1983) J. Virol. 46,661-666 PAA, phosphonoacetic acid. 10. O’Donnell, M. E., Elias, P., Funnell, B. E., and Lehman, I. R. (1987) J. Bwl. Chem. 262,4260-4266 It is not surprisingthat t h e 3 ‘ 4 5 ‘ exonuclease and polym- 11. Eisenberg, S., Harbers, B.. Hours,. C... and Denhardt. D. T. (1975) . . J. Mol.-koi. 99, 107-123 erase activities share the same polypeptide chain. Other po12. Aposhian, H. V., and Kornberg, J. Biol. Chem. 237. -. A. (1962) . lymerases with associated exonuclease activity have both ac519-525 tive sites on a single polypeptide (1). However, the roughly 13. Soltis, D. A., and Lehman, I. R. (1983) J. Bwl. Chem.258,6073equal sensitivity of the herpes polymeraseand 3‘+5‘ exonu6077 clease activities to inhibition by phosphonoacetic acid during 14. McHenry, C., and Kornberg, A. (1977)J. Biol. Chem. 252,64786484 DNA synthesis was unexpected. In the case of the E. coli DNA polymerase I large fragment (31), crystallographic anal- 15. Panasenko, S. M., Alazard, R. J., and Lehman, I. R. (1978) J. Bwl. Chem. 253,4590-4592 ysis has demonstrated that the two active sitesare physically 16. Post, L. E., Mackem, M., and Roizman, B. (1981) Cell 24, 555separated from each other by approximately 25A (32). Pos565 sibly,phosphonoaceticacidbindstooneactivesite and 17. Elias, P., O’Donnell, M. E., Mocarski, E. S., and Lehman, I. R. (1986) Proc. Natl. Acad. Sci. U. S. A. 83, 6322-6326 thereby prevents switching of the primer 3‘ terminus to the 18. Alberts, B., and Herrick, G. (1970) Methods Enzymol. 23, 1908other site. 1917 The herpes polymerase differs in many important respects 19. Laemmli, U.K. (1970) Nature 227,680-685 from DNA polymerase (Y (Table 111). These differences may 20. Read, M., and Northcote, D. H. (1981) Anal. Biochem. 116,53reflect differences inthe complexity of replicating host chro64 mosomes organized into a complex nucleosomal structure as 21. Sanger, F., Coulson, A. R., Friedmann, T., Air, G. M., Barrell, B. compared with the relatively simple 150-kb HSV-1 genome. G., Brown, N. L., Fiddes, J. C., Hutchison, C. A., 111, Slocombe, P. M., and Smith, M. (1978) J. Mol. Biol. 125,225-246 In both cases, however, the DNA polymerase is very likely that could very 22. O’Donnell, M. E., and Kornberg, A. (1985) J. Bwl. Chem. 260, associated with accessory replication proteins 12875-12883 significantly alter their catalytic properties. 23. Lehman, I. R. (1974) Science 186, 790-797 Acknowledgment-We are grateful to Ed Mocarski for expert ad- 24. Weissbach, A., Hong, S.-C. H., Aucker, J., and Muller, R. (1973) J. Biol. Chem. 248,6270-6277 vice and assistance in the handling of cells and viruses. HSV-1 DNA

DNA

polymerase

polymerase a’

HSV-1 DNA Polymerase 25. Knouf. K.-W. (1979) Eur. J. Biochem. 98. 231-244 30. 26. BenlPorat, T.,Blankenship, M. L., DeMarchi, J. M., and Kaplan, A. S. (1977) J. Virol. 2 2 , 734-741 27. Blumenthal, A. B., Kriegstein, H. J., and Hogness, D. S. (1973) Cold Spring Harbor Symp. Qwnt.Bwl. 3 8 , 205-22332. 28. Huberman, J. A., and Riggs, A. D. (1968) J. Mol. Biol. 32, 327-

4259

Deleted proof in 31. Setlow, P., Brutlag, D., and Kornberg, A. (1972) J. Biol. Chem. 247,224-231

Ollis, D. L., Brick, P., Hamlin, R., Xhong, N. G., and Steitz, T. A. (1985) Nature 313, 762-766