DNA primase activity associated with DNA polymerase alpha from Xenopus laevis ovaries.

One of the two forms of DNA polymerase alpha from ovaries of the frog Xenopus laevis catalyzed ribonucleoside triphosphate-dependent DNA synthesis on single-stranded circular fd phage DNA templates. DNA synthesis was dependent on ATP and added template. CTP, GTP, and UTP stimulated DNA synthesis but were not required and could not substitute for ATP. DNA synthesis was not inhibited by alpha-amanitin. Neither poly(dT) nor double-stranded DNA served as template. Analysis of [32P]-dTMP-labeled product by neutral and alkaline agarose gel electrophoresis showed that 0.1- to 1-kilobase DNA fragments (average size of approximately equal to 0.25 kilobase) were synthesized. The fragments were not covalently linked to the template. Either [alpha-32P]NMP, [gamma-32P]ATP, or [gamma-32P]GTP were incorporated also into the product. Analysis of the product after hydrolysis by KOH, alkaline phosphatase, or bacteriophage T4 3' leads to 5' exonuclease showed the presence of a small oligoribonucleotide primer at the 5' end of the newly synthesized DNA. NTP-dependent DNA-synthesizing activity copurified on six columns and cosedimented during glycerol gradient centrifugation with one form of DNA polymerase alpha activity but not with the other form. These results suggest that DNA primase activity is associated with one of the two forms of X. laevis DNA polymerase alpha.     

RNA-primed DNA synthesis: specific catalysis by HeLa cell DNA polymerase alpha.

We have analyzed and compared the responses of the three major HeLa cell DNA polymerases (alpha, beta, and gamma) to a HeLa DNA template with short RNA or DNA primers hybridized to it. Only DNA polymerase alpha is able to synthesize DNA covalently bonded to the RNA primer via a 3' yields 5' phosphodiester bond. 32P transfer experiments showed that all combinations of ribo- and deoxyribonucleotides are represented in the RNA-DNA linkages but their distribution is nonrandom. The RNA-DNA linked molecules base-paired to a HeLa DNA template strand represent a possible "natural" in vitro primer-template for DNA polymerases and can be extended by all three DNA polymerases (alpha, beta, and gamma). These findings indicate that DNA polymerases beta and gamma are capable of DNA-primed but not RNA-PRIMED DNA synthesis, while DNA polymerase alpha is capable of both RNA-primed and DAN-primed DNA synthesis.     

Synthesis by the DNA primase of Drosophila melanogaster of a primer with a unique chain length.

The primase associated with the DNA polymerase alpha from embryos of Drosophila melanogaster catalyzes the synthesis of ribo-oligonucleotide primers on single-stranded M13 DNA or polydeoxythymidylate templates, which can be elongated by DNA polymerase action [Conaway, R. C. & Lehman, I. R. (1982) Proc, Natl. Acad. Sci, USA 79, 2523--2527]. The primers synthesized in a coupled primase-DNA polymerase alpha reaction with an M13 DNA template are of a unique size (15 residues); those synthesized with poly(dT) range from 8 to 15 nucleotides. Primer synthesis is initiated at multiple but nonrandom sites. Like the DNA primase of Escherichia coli and the comparable activity in intact nuclei of polyoma-infected mouse cells, the DNA primase of D. melanogaster can substitute deoxynucleotides for ribonucleotides during primer synthesis.     

A DNA primase activity associated with DNA polymerase alpha from Drosophila melanogaster embryos.

Preparations of DNA polymerase alpha from early embryos of Drosophila melanogaster catalyze the ATP-dependent synthesis of DNA with single-stranded M13 DNA or poly(dT) templates. In the case of M13 DNA, GTP, but not UTP or CTP, can replace ATP. The reaction is completely dependent on added template and is not inhibited by alpha-amanitin. Alkaline hydrolysis of the product synthesized in the presence of [alpha-32P]dATP and poly(dT) generates 32P-labeled 3'(2') adenylate, showing that a covalent ribo-deoxynucleotide linkage is formed. Furthermore, incorporation of ribonucleotides occurs at the 5' end of the newly synthesized polynucleotide chain. These findings are consistent with the hypothesis that a ribo-oligonucleotide primer is synthesized by primase action and subsequently elongated by DNA polymerase. Under the appropriate conditions, DNA polymerase I from Escherichia coli can elongate primers formed by primase in the presence of ATP and poly(dT). Primase activity copurifies with DNA polymerase alpha and may be part of the multisubunit polymerase molecule.     

Inhibition of the DNA Polymerase of Rauscher Leukemia Virus by Single-Stranded Polyribonucleotides

The DNA polymerase of Rauscher murine leukemia virus is strongly and specifically inhibited by nontemplate, single-stranded polyribonucleotides with either the resident viral RNA, native calf-thymus DNA, or poly[d(A-T)] as templates. These inhibitory homopolymers are apparently bound to the template site of the polymerase, since they interact competitively with the template. The strength of the inhibition depends on the particular homopolymer used: poly(U) > poly(G) > poly(A) > poly(C). The K(i) for poly(U) was 0.08 mug/ml, which represents an apparent affinity six times greater than that observed for viral RNA. No such inhibition was observed with a highly purified DNA polymerase from mouse embryos or the Escherichia coli enzyme.     

DNA polymerase delta from embryos of Drosophila melanogaster.

We have purified a DNA polymerase activity from 0- to 2-hr embryos of Drosophila melanogaster to near homogeneity. The purified enzyme consists of a single 120-kDa polypeptide, which contains polymerase and 3'-->5' exonuclease activities. Exonuclease activity is inhibited by deoxynucleoside triphosphates, suggesting that the polymerase and exonuclease activities are coupled. The polymerase is more active with poly(dA-dT) than with activated DNA or poly(dA)/oligo(dT) as template. It shows a low degree of processivity with poly(dA)/oligo(dT). The polymerase is sensitive to aphidicolin and carbonyldiphosphonate but resistant to N2-[p-(n-butyl)phenyl]-2-deoxyguanosine triphosphate, 2-[p-(n-butyl)anilino]-2-deoxyadenosine triphosphate, and dideoxythymidine triphosphate. The 120-kDa polypeptide can be distinguished from the large subunit of Drosophila DNA polymerase alpha on the basis of the peptides generated by partial cleavage with N-chlorosuccinimide and by its failure to react with a monoclonal antibody directed against the large subunit of DNA polymerase alpha. The DNA polymerase is inhibited by 200 mM NaCl and is unable to use poly(rA)/oligo(dT) as a template, thus differentiating it from DNA polymerase gamma. On the basis of these properties, we propose that the DNA polymerase that we have purified from 0- to 2-hr Drosophila melanogaster embryos is DNA polymerase delta.     

Incorporation into DNA of the base analog 2-aminopurine by the Epstein-Barr virus-induced DNA polymerase in vivo and in vitro.

The Epstein-Barr virus (EBV)-induced intracellular DNA polymerase was assayed in vitro for the ability to utilize the mutagenic nucleotide analog 2-aminopurine deoxyribose triphosphate (d2apTP), incorporating it as the corresponding monophosphate into DNA or poly[d)(A-T)] template. Bacteriophage T4, lymphocyte alpha, and the EBV particle-associated DNA polymerases were assayed simultaneously for direct comparison. Unlike these three polymerases, which were capable of distinguishing between d2apTP and dATP with a strong preference for the latter, the EBV-induced DNA polymerase only weakly distinguished between dATP and d2apTP and incorporated substantial amounts of d2apTP into template. Detergent-treated lymphocyte nuclei undergoing a high level of EBV DNA synthesis were shown to incorporate the 2-aminopurine analog of dATP into viral DNA. The relative inability of the EBV-induced DNA polymerase to distinguish between the two purine nucleotides reported here is consistent with previous reports on the ready incorporation of other nucleotide analogs into DNA polymerases induced by other herpesviruses. Because most antiherpes agents currently in use or under study are nucleotide analogs, the viral mutagenic properties of these drugs should be examined.     

Accessory proteins for DNA polymerase alpha activity with single-strand DNA templates

Three forms of DNA polymerase alpha [DNA nucleotidyltransferase (DNA-directed), EC 2.7.7.7] were partially purified from the combined nuclear extract and postmicrosomal supernatant solution of synchronized HeLa cells. These enzymes, designated DNA polymerases alpha 1, alpha 2, and alpha 3, on the basis of their order of elution from DEAE-Bio-Gel, differ in their abilities to utilize single-strand DNA templates. DNA polymerase alpha 2 has equal catalytic activities with activated and single-strand DNAs as template-primers. DNA polymerase alpha 1 has only partial catalytic activity with single-strand DNA templates, and DNA polymerase alpha 3 is essentially inactive with this template. Successive steps of hydrophobic affinity chromatography and phosphocellulose chromatography of DNA polymerase alpha 2 resolved the polymerase alpha activity and two protein factors (C1 and C2) that are required for its catalytic activity with a DNA template-primer that contains extended single-strand regions. In the absence of the factors, DNA polymerase alpha activity is measurable with activated but not single-strand DNA templates. In the presence of the C1 and C2 factors DNA polymerase alpha activity with single-strand DNA templates is restored to about 75% of the catalytic activity of DNA polymerase alpha 2 with this template.     

Inhibition of DNA synthesis by an electrophilic metabolite of benzo[a]pyrene.

Mitogen-stimulated scheduled DNA synthesis and DNA excision repair in human lymphocytes, as well as DNA polymerase a activity in a cell-free system, were inhibited by an electrophilic metabolite of benzo[a]pyrene. This metabolite, (+/-)-anti-(7r,8t)-dihydroxy-(9,10t)-epoxy-7,8,9,10-tetrahyd robenzo[a]pyrene (BPDE), covalently binds to cellular macromolecules and is mutagenic, carcinogenic, and cytotoxic. Human lymphocytes treated with BPDE at concentrations greater than 500-800 ng/ml showed decreases in both mitogen-stimulated DNA synthesis and excision repair of damaged DNA but did not exhibit overt cytotoxicity (excluded trypan blue and maintained an adenylate charge of greater than 0.7). Formation of, and total concentration of, BPDE-DNA adducts was not correlated with inhibition of DNA synthesis. DNA polymerase alpha studies using a cell-free system showed that enzymatic activity was not diminished when purified polymerase was treated with BPDE prior to the addition of template DNA. When the template DNA concentration was varied, BPDE inhibition of enzyme activity was uncompetitive. BPDE inhibition of enzyme activity was found to be noncompetitive when concentrations of dATP, dCTP, or dTTP were varied and competitive when the concentration of dGTP was varied. The data indicate that BPDE competitively inhibits interaction of dGTP with the template-DNA polymerase alpha complex.     

Poly(ADP-Ribose): Release of Template Restriction in HeLa Cells

Evidence is presented to show that ADP-ribosylation of nuclear proteins by poly(ADP-ribose) polymerase enhances template-primer activity of HeLa cell nuclear DNA. We used Escherichia coli DNA polymerase I (EC 2.7.7.7; DNA nucleotidyltransferase) as an exogenous probe of nuclear DNA status. Neither NAD nor free poly(ADP-ribose) acts directly on the bacterial enzyme. The stimulation is specific for formation of ADP-ribosylated proteins and is not a generalized polyanion or nucleotide effect on chromatin. The release of template restriction is proportional to the capacity of a given cell line to synthesize poly(ADP-ribose); both the stimulation and poly(ADP-ribose) formation are coordinately proportional to NAD concentration. Binding studies with DNA polymerase indicate exposure or generation of additional 3'-OH primer sites due to ADP-ribosylation in intact nuclei. With intact cells, there appears a correlation among growth, physiological template restriction, and the above effects of ADP-ribosylation.     

Mechanism of ultraviolet-induced mutagenesis: Extent and fidelity of in vitro DNA synthesis on irradiated templates

The effect of UV irradiation on the extent and fidelity of DNA synthesis in vitro was studied by using homopolymers and primed single-stranded varphiX174 phage DNA as substrates. Unfractionated and fractionated cell-free extracts from Escherichia coli pol(+) and polA1 mutants as well as purified DNA polymerase I were used as sources of enzymatic activity. (DNA polymerases, as used here, refer to deoxynucleosidetriphosphate:DNA deoxynucleotidyltransferase, EC 2.7.7.7.) The extent of inhibition of DNA synthesis on UV-irradiated varphiX174 DNA suggested that pyrimidine dimers act as an absolute block for chain elongation by DNA polymerases I and III. Experiments with an irradiated poly(dC) template failed to detect incorporation of noncomplementary bases due to pyrimidine dimers. A large increase in the turnover of nucleoside triphosphates to free monophosphates during synthesis by DNA polymerase I on irradiated varphiX174 DNA has been observed. We propose that this nucleotide turnover is due to idling by DNA polymerase (i.e., incorporation and subsequent excision of nucleotides opposite UV photolesions, by the 3'-->5' "proofreading" exonuclease) thus preventing replication past pyrimidine dimers and the potentially mutagenic event that should result. In support of this hypothesis, DNA synthesis by DNA polymerase from avian myeloblastosis virus and by mammalian DNA polymerase alpha, both of which are devoid of any exonuclease activity, was found to be only partially inhibited, but not blocked, by UV irradiation of the template and accompanied by an increased incorporation of noncomplementary nucleotides. It is suggested that UV mutagenesis in bacteria requires an induced modification of the cellular DNA replication machinery, possibly an inhibition of the 3'-->5' exonuclease activity associated with DNA polymerases.     

On the mechanism of selective inhibition of herpesvirus replication by (E)-5-(2-bromovinyl)-2''-deoxyuridine

Bromovinyldeoxyuridine (BVdUrd) is a potent antiherpesvirus compound with low cytotoxicity. To gain an insight into its selectivity and mechanism of inhibition, we chemically synthesized the 5'-triphosphate of BVdUrd, BVdUTP, and tested its effect on the activities of DNA polymerases [DNA nucleotidyltransferase (DNA directed), EC 2.7.7.7] of two herpesviruses--i.e., herpes simplex virus type 1 (HSV-1) and Epstein-Barr virus (EBV)--as well as cellular DNA polymerases alpha, beta, and gamma. The effects on the DNA polymerases were determined under assay conditions optimal for the individual polymerases. We found that the BVdUTP was considerably more inhibityory to the utilization of dTTP by the HSV-1 DNA polymerase then by the cellular DNA polymerases. For instance, as little as 1 microM BVdUTP inhibited the utilization of dTTP by HSV-1 DNA polymerase 50%, whereas the same concentration inhibited the DNA polymerase alpha and the DNA polymerase beta activities only 9% and 3%, respectively. The BVdUTP inhibited DNA synthesis by competing with the natural substrate, dTTP. The Km for dTTP and the Ki for the BVdUTP of the HSV-1 DNA polymerase were 0.66 and 0.25 microM, respectively. Kinetic analyses with the DNA polymerases alpha and beta and the EBV DNA polymerase also reflected a similar difference in sensitivity between the HSV-1 enzyme and other enzymes. Increasing the concentration of either the DNA template or the enzyme in the reaction mixture did not bring about a significant change in the extent of inhibition. Preincubation of the inhibitor with the enzyme was not necessary for inhibition. Studies on time course of inhibition revealed that the compound is inhibitory even after the initiation of DNA synthesis. These studies indicate that the ability of BVdUTP to preferentially inhibit the HSV-1 DNA polymerase may contribute towards its selective inhibition of the viral DNA replication in infected cells.     

Model system for DNA replication of a plasmid DNA containing the autonomously replicating sequence from Saccharomyces cerevisiae.

A negatively supercoiled plasmid DNA containing autonomously replicating sequence (ARS) 1 from Saccharomyces cerevisiae was replicated with the proteins required for simian virus 40 DNA replication. The proteins included simian virus 40 large tumor antigen as a DNA helicase, DNA polymerase alpha.primase, and the multisubunit human single-stranded DNA-binding protein from HeLa cells; DNA gyrase from Escherichia coli, which relaxes positive but not negative supercoils, was included as a "swivelase." DNA replication started from the ARS region, proceeded bidirectionally with the synthesis of leading and lagging strands, and resulted in the synthesis of up to 10% of the input DNA in 1 h. The addition of HeLa DNA topoisomerase I, which relaxes both positive and negative supercoils, to this system inhibited DNA replication, suggesting that negative supercoiling of the template DNA is required for initiation. These results suggest that DNA replication starts from the ARS region where the DNA duplex is unwound by torsional stress; this unwound region can be recognized by a DNA helicase with the assistance of the multisubunit human single-stranded DNA-binding protein.     

Role of DNA polymerase alpha and DNA primase in simian virus 40 DNA replication in vitro.

The role of DNA polymerase alpha (pol alpha) and DNA primase has been investigated in the simian virus 40 (SV40) DNA replication system in vitro. Removal of pol alpha and primase activities from crude extracts of HeLa cells or monkey cells by use of an anti-pol alpha immunoaffinity column resulted in the loss of replication activity. The addition of purified pol alpha-primase complex isolated from HeLa cells or monkey cells restored the replication activity of depleted extracts. In contrast, the pol alpha-primase complex isolated from either mouse cells or calf thumus did not. Extracts prepared from mouse cells (a source that does not support replication of SV40) did not replicate SV40 DNA. However, the addition of purified pol alpha-primase complex isolated from HeLa cells activated mouse cell extracts. pol alpha and primase from HeLa cells were extensively purified and separated by a one-step immunoaffinity adsorption and elution procedure. Both activities were required to restore DNA synthesis; the addition of pol alpha or primase alone supported replication poorly. Crude extracts of HeLa cells that were active in SV40 replication catalyzed the synthesis of full-length linear double-stranded (RFIII) DNA in reaction mixtures containing poly(dT)-tailed pBR322 RFIII. Maximal activity was dependent on the addition of oligo(dA), ATP, and creatine phosphate and was totally inhibited by aphidicolin. Since pol alpha alone could not replicate this substrate and since there was no degradation of input DNA, we propose that other enzymatic activities associate with pol alpha, displace the non-template strand, and allow the enzyme to replicate through duplex regions.     

Stimulation of human neuroblastoma DNA polymerase alpha and primase activities by a protein factor isolated from rat liver chromatin.

Nuclear protein factor type 1 (NPF-1) that simulates IMR-32 primase-associated DNA polymerase alpha 1 and alpha 2 activities has been purified from a high-salt extract of liver chromatin from 6-month-old rats. The final purified factor lacks DNA polymerase alpha, RNA polymerase, and DNA-unwinding or topoisomerase type I activities. The stimulatory activity is destroyed by trypsin (60 min at 37 degrees C), DNase II (60 min at 37 degrees C), and heat treatment (2 min at 68 degrees C). The 125I-labeled NPF-1 does not bind to activated calf thymus DNA or poly(dC). However, it forms a ternary complex with DNA in the presence of DNA polymerase alpha-primase complex (alpha 1 and alpha 2). The ternary complex sediments on sucrose density gradient as a heavier band (11S). The NPF-1 also stimulates (2.5-fold) primase-catalyzed incorporation of GMP and dGMP from the corresponding triphosphates on poly(dC) template even in the presence of a high concentration of alpha-amanitin (400 micrograms/ml). The labeled duplex containing the poly(dC) template, [32P]-GTP, and [3H]dGTP loses 80% of the 32P label and 70% of the 3H label after treatment with 0.3 M KOH and DNase I, respectively. The products were isolated from reaction mixtures incubated with and without NPF-1 and subjected to alkaline sucrose-density-gradient sedimentation analysis. The results suggest that the rate of synthesis of DNA short chains is increased in the presence of NPF-1 without a concomitant increase in the chain length of the newly synthesized products.     

Elongation of primed DNA templates by eukaryotic DNA polymerases.

The combined action of DNA polymerase alpha and DNA polymerase beta leads to the synthesis of full-length linear DNA strands with phi X174 DNA templates containing an RNA primer. The reaction can be carried out in two stages. In the first stage, DNA polymerase alpha catalyzes the synthesis of a chain that averaged 230 deoxynucleotides long and was covalently linked to the RNA primer. In the second stage, DNA polymerase beta elongates the DNA strand covalently attached to the RNA primer to full length. With DNA primers, DNA polymerase alpha catalyzes only limited deoxynucleotide addition whereas DNA polymerase beta alone elongates DNA primed templates to full length. DNA polymerase beta can also stimulate the synthesis of adenovirus DNA in vitro in the presence of a cytosol extract from adenovirus-infected cells. In all of these systems, dNMP incorporation catalyzed by DNA polymerase beta was sensitive to N-ethylmaleimide; however, this polymerase activity was resistant to N-ethylmaleimide with poly(rA) x (dT) as the primer template.     

Adenovirus DNA replication in vitro: purification of the terminal protein in a functional form.

The 80,000-dalton form of the adenovirus (Ad) terminal protein (pTP) has been purified from Ad-infected HeLa cells. pTP was assayed by its ability to form a covalent complex with dCMP. The protein copurified with an activity that is essential for in vitro Ad DNA replication (Ad protein activity) as well as with a DNA polymerase activity that was distinguished from those of HeLa cell DNA polymerases alpha, beta, and gamma. The Ad protein-associated DNA polymerase activity was detected with activated DNA but not with poly(rA).oligo(dT) as template and was insensitive to aphidicolin and sensitive to N-ethylmaleimide. The Ad protein, DNA polymerase, and pTP-dCMP complex-forming activities sedimented in a glycerol gradient as a single peak with an apparent molecular size of 180,000 daltons. NaDodSO4/polyacrylamide gel analysis of the glycerol gradient fraction showed major bands of 80,000 and 140,000 daltons. The 80,000-dalton band was identified as pTP by comparison of its tryptic peptide map with that of the 55,000-dalton form of the terminal protein, which was purified from Ad virions.     

Isolation of a herpesvirus-specific DNA polymerase from tissues of an American patient with Burkitt lymphoma.

A DNA polymerase (DNA nucleotidyltransferase) has been partially purified from a neck mass of an American patient with Burkitt lymphoma and separated from the cellular DNA polymerases. The molecular weight of the enzyme was approximately 90,000. The enzyme differs from the cellular DNA polymerases, but resembles herpes-virus-induced DNA polymerase in its primer template preference, high monovalent cation requirement for activity, and sensitivity to phosphonoacetate. Enzyme activity was inhibited specifically by an antibody directed against herpes-simplex-virus-induced DNA polymerase but not by antibodies directed against DNA polymerase alpha of HeLa cells and DNA polymerase gamma of a normal human lymphoblast cell line, NC37. Although serum of the patient with Burkitt lymphoma contained high Epstein-Barr virus titer, addition of the serum to the assay mixture did not have any effect on the activity of Burkitt lymphoma DNA polymerase. Tissues from spleen and liver of the patient with Burkitt lymphoma did not contain the herpes-virus-induced DNA polymerase. Detection of the herpes virus polymerase in the Burkitt lymphoma tissue provides additional evidence for the association of Epstein-Barr virus with this malignancy.