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S Izuta

Publications and source records attributed to S Izuta.

At least 37 records · Page 2Linked to original sources
PubMed1994

DNA polymerase alpha overcomes an error-prone pause site in the presence of replication protein-A.

Eukaryotic DNA polymerase alpha pauses at some sites on the natural DNA template of M13mp2. Terminal misincorporations of dA or dG, in place of dT, by DNA polymerase alpha have been reported to be within one of the pause sites, pause site II (positions 6269 and 6270 (Fry, M., and Loeb, L.A. (1992) Proc. Natl. Acad. Sci. U.S.A. 89, 763-767)). The DNA products arrested within pause site II (position 6270) were separated, annealed with synthetic templates, and further elongated by DNA polymerase alpha. It was confirmed that a considerable amount of terminal misincorporation of dG in place of dT occurred at this position. When M13mp2 DNA was coated with various amounts of replication protein-A (RP-A), however, DNA polymerase alpha was able to overcome the pause site II, whereas pause bands at other sites barely decreased. In contrast, Escherichia coli single-stranded DNA-binding protein did not specifically abolish the arrested band at pause site II, though it generally suppressed the reaction. Since RP-A hardly increased the elongation frequency from the primer carrying a 3'-mismatched terminal deoxynucleotide, the reduction of arrested products by RP-A may be attributed to the change in the incorporation mode from noncomplementary to complementary deoxynucleotides within pause site II and may not be due to the reinitiation from the mismatched 3'-terminal deoxynucleotide. To confirm this, we amplified the reaction products at pause site III by means of a polymerase chain reaction method and showed that the complementary strand to pause site II, which was elongated in the presence of RP-A, did not carry any detectable misinsertion. Therefore, the errorprone step of the DNA synthesis catalyzed by DNA polymerase alpha may be readily avoided by RP-A.

Animals↗
PubMed1994

Mispair-, site-, and strand-specific error rates during simian virus 40 origin-dependent replication in vitro with excess deoxythymidine triphosphate.

We have measured the fidelity of leading and lagging strand DNA replication in HeLa cell extracts. Providing an excess of one dNTP in reactions induces replication errors consistent with misincorporation of that dNTP. With excess dTTP, both substitutions and single-nucleotide frameshifts are induced. Error distribution is nonrandom; reproducible hot spots for a substitution and a frameshift error are observed. Measurements with two vectors having the origin of replication on opposite sides of the mutational target demonstrate that error rates for G.dTTP and C.dTTP mispairs depend on whether the strand is replicated as the leading or lagging strand. Also, the two hot spots are only observed in one origin-target orientation. Replication reactions reconstituted from two fractions derived from extracts are 3-fold less accurate, but the error specificity with excess dTTP is similar to that with extracts. This suggests that the processes responsible for the nonrandom error rates are not lost as a result of fractionation. Furthermore, the reconstituted system is devoid of mismatch repair activity. Thus, mismatch repair is not responsible for the mispair-, site-, and strand-specific differences observed.

Base Sequence↗
PubMed1993

RNA priming coupled with DNA synthesis on natural template by calf thymus DNA polymerase alpha-primase.

A bovine genomic DNA library was surveyed with respect to the template activity for RNA-primed DNA synthesis by calf thymus DNA polymerase alpha-primase complex. About 7% of the single-stranded DNA clones contained distinct initiation sites consisting of pyrimidine clusters of pyrimidine-rich sequences. The initiation sites were located at or near the 3'-end of the pyrimidine clusters. One of these sequences, containing a 10-mer pyrimidine cluster with major initiation sites, was analyzed in detail. By the successive substitutions of pyrimidines in the cluster with oligodeoxydenylate [(dA)n] in the 5' to 3' direction, the minimum length of the initiation sequence was estimated to be as long as the 7-mer. In contrast, when one or three pyrimidines at the 3'-end of the cluster were replaced with (dA)n, the priming activity was largely lost, indicating that these pyrimidine residues were indispensable for priming. Furthermore, base substitutions of upstream or downstream sequences outside the pyrimidine cluster also decreased the total priming frequencies. Interestingly, the base substitutions inside or outside of the pyrimidine cluster sometimes caused a shift in the major priming sites. These results indicate that the minimum priming unit of the CTPPS1 template for RNA-primed DNA synthesis consists of a pyrimidine cluster (6-mer) with one purine at its 3'-border and that both the 3'-downstream 6-bases and the 5'-upstream 17-bases modulate the priming by enhancing the priming frequency and/or slightly shifting the sites of initiation of primer synthesis. It was also revealed that the lengths of the product RNA primers became shorter as the length of pyrimidine cluster was shortened by substitution with (dA)n. The gel retardation assay further showed that the complex formation between DNA polymerase alpha-primase and the DNA templates was strongly in competition with poly(dC), poly(dG), and poly(dT) but not with poly(dA). Furthermore, template activities as well as the pyrimidine contents of a series of base-substituted DNA correlated well with their affinities to the enzyme, as measured by both gel retardation assay and their Km values for the priming reaction. Apparently, DNA polymerase alpha-primase primarily recognizes the minimum priming unit consisting of a pyrimidine cluster with a purine at the 3'-boundary of purine, but the initiation of primer RNA synthesis can be modified by pyrimidine residues outside of the minimum priming unit.

Adenosine Triphosphate↗
PubMed1993

Poly(ADP-ribose) polymerase stimulates DNA polymerase alpha by physical association.

The direct effect of the eukaryotic nuclear DNA-binding protein poly(ADP-ribose) polymerase on the activity of DNA polymerase alpha was investigated. Homogenously purified poly(ADP-ribose) polymerase (5 to 10 micrograms/ml) stimulated the activity of immunoaffinity-purified calf or human DNA polymerase alpha by about 6 to 60-fold in a dose-dependent manner. It had no effect on the activities of DNA polymerase beta, DNA polymerase gamma, and primase, indicating that its effect is specific for DNA polymerase alpha. Apparently, poly(ADP-ribosyl)ation of DNA polymerase alpha was not necessary for the stimulation. The stimulatory activity is due to poly(ADP-ribose) polymerase itself since it was immunoprecipitated with a monoclonal antibody directed against poly(ADP-ribose) polymerase. Kinetic analysis showed that, in the presence of poly(ADP-ribose) polymerase, the saturation curve for DNA template primer became sigmoidal; at very low concentrations of DNA, it rather inhibited the reaction in competition with template DNA, while, at higher DNA doses, it greatly stimulated the reaction by increasing the Vmax of the reaction. By the automodification of poly(ADP-ribose) polymerase, however, both the inhibition at low DNA concentration and the stimulation at high DNA doses were largely lost. Furthermore, stimulation by poly(ADP-ribose) polymerase could not be attributed to its DNA-binding function alone since its fragment, containing only the DNA-binding domain, could not exert full stimulatory effect on DNA polymerase, as of the intact enzyme. Poly(ADP-ribose) polymerase is co-immunoprecipitated with DNA polymerase alpha, using anti-DNA polymerase alpha antibody, clearly showing that poly(ADP-ribose) polymerase may be physically associated with DNA polymerase alpha. In a crude extract of calf thymus, a part of poly(ADP-ribose) polymerase activity existed in a 400-kDa, as well as, a larger 700-kDa complex containing DNA polymerase alpha, suggesting the existence in vivo of a complex of these two enzymes.

Animals↗
PubMed1993

Deoxypyrimidine cluster mediates the priming by calf thymus DNA primase subunit.

Homogeneously purified DNA polymerase alpha subunit-free primase was used to analyze primer RNA synthesis. On a chemically synthesized 36 mer DNA template, a part of upstream region of human c-myc gene, the primer synthesis started from a doublet of deoxythymidine (TT) in the deoxypyrimidine-rich sequence. The primase in DNA polymerase alpha-primase complex synthesized 21-mer reaction product, while DNA polymerase alpha-free primase gave the similar products, 21- and 22-mer, indicating that the site recognition was carried out by primase itself and DNA polymerase alpha subunit has an auxiliary role on it. Product analysis using DNA fragments carrying base substitutions further revealed that the existence of deoxypyrimidine residues around the starting sites was important for priming frequencies. Competition analysis showed that the priming was strongly competed by poly(dC), and to a much lesser extent by poly(dA). Gel-shift analysis showed that the primase could bind to the DNA template, and this complex formation was also competed by poly(dC), but not by poly(dA). These results indicate that primase subunit interacts with the starting site by binding directly with deoxypyrimidine residues.

Animals↗
PubMed1992

Inhibitory effects of triphosphate derivatives of oxetanocin G and related compounds on eukaryotic and viral DNA polymerases and human immunodeficiency virus reverse transcriptase.

In order to clarify the biological activities of (-)-oxetanocin G, and (-)-oxetanocin A and its carbocyclic analogue, (-)-carboxetanocin G, the inhibitory effects of triphosphate derivatives of these compounds (OXT-GTP, OXT-ATP, and C-OXT-GTP) on eukaryotic and viral DNA polymerases were examined. DNA polymerase alpha purified from calf thymus was weakly inhibited by OXT-GTP and OXT-ATP but strongly by C-OXT-GTP, the Ki value being 0.22 microM. On the other hand, rat DNA polymerase beta was not affected by these analogues. DNA polymerase gamma purified from bovine testes was very weakly inhibited by OXT-GTP and OXT-ATP, but not by C-OXT-GTP. DNA polymerase from herpes simplex virus type-II (HSV-II) was strongly inhibited by all three analogues, the Ki values ranging from 0.5 to 1.0 microM. Human immunodeficiency virus-encoded reverse transcriptase (HIV RT) was also strongly inhibited by these three analogues, the Ki value of C-OXT-GTP being slightly smaller than that of OXT-GTP or OXT-ATP. Analysis of products synthesized on singly primed M13 single-stranded DNA by DNA polymerase alpha, HSV-II DNA polymerase or HIV RT in the presence of the analogues revealed that OXT-GTP and C-OXT-GTP were incorporated into DNA and caused chain termination mainly at sites one or two nucleotides beyond the cytosine bases on the template.

Adenine↗
PubMed1992

Inhibitory effects of 2'-deoxy-5-styryluridine 5'-triphosphate analogs on retroviral reverse transcriptase and eukaryotic DNA polymerases.

Some sugar modified analogs of 2'-deoxy-E-5-styryluridine triphosphates were synthesized and examined for their inhibitory effects on eukaryotic DNA polymerases and HIV-1 reverse transcriptase. Among these compounds, 3'-azido-2',3'-dideoxy-E-5-styrylUTP (6) and 2',3'-dideoxy-E-5-styrylUTP (7) showed remarkable inhibitory effects on reverse transcriptase. The mode of action and the influence of the substituent at C-5 of 2',3'-dideoxyUTP analogs will be described.

Eukaryotic Cells↗
PubMed1991

The 5'-triphosphates of 3'-azido-3'-deoxythymidine and 2', 3'-dideoxynucleosides inhibit DNA polymerase gamma by different mechanisms.

Inhibition mechanisms of 5'-triphosphates of 3'-azido-3'-deoxythymidine (AZT-TP) and 3'-deoxythymidine (ddTTP) on extensively purified DNA polymerase gamma from bovine testes were examined by analysis of the products synthesized on singly primed M13 single-stranded DNA or synthetic oligonucleotide template-primer in the presence of analogues. The results indicate that AZT-TP inhibits DNA polymerase gamma in competition with dTTP but is not incorporated into DNA, whereas ddTTP is incorporated into DNA and causes chain termination. In contrast, both analogues were used by reverse transcriptase and caused chain termination.

Animals↗
PubMed1991

Glutathione levels and related enzyme activities in vitamin B-6-deficient rats fed a high methionine and low cystine diet.

We examined the change in glutathione metabolism in vitamin B-6-deficient rats. Vitamin B-6-deficient rats were fed a vitamin B-6-deficient diet containing 0.56% methionine and 0.075% cystine for 8 wk. Controls were fed an identical diet supplemented with 10 mg pyridoxine hydrochloride/kg diet. Glutathione concentrations in each organ examined were similar in control and vitamin B-6-deficient rats, and the values were comparably lower after intraperitoneal injection of diethylmaleate. However, buthionine sulfoximine caused a significantly greater decrease in glutathione levels in the liver and lungs of vitamin B-6-deficient rats relative to controls. Glutathione peroxidase activity in the liver of vitamin B-6-deficient rats was higher than in control animals; however, glutathione transferase activity in tissues other than liver of vitamin B-6-deficient rats was higher than in the controls. The activities of gamma-glutamyl-transferase in the liver and spleen of vitamin B-6-deficient rats were significantly lower than control values. The holoenzyme activities of cystathionine beta-synthase and cystathionine gamma-lyase in the liver of vitamin B-6-deficient rats were markedly reduced. These findings indicate that although the activities of enzymes that synthesize cysteine from methionine were decreased by vitamin B-6 deficiency, the level of synthesis and supply of cysteine in vitamin B-6-deficient rats were sufficient to maintain the same glutathione level as in controls, and that glutathione utilization in the liver was accelerated by vitamin B-6 deficiency.

Animals↗
PubMed1991

Sequence-dependent termination of mammalian DNA polymerase reaction by a new platinum compound, (-)-(R)-2-aminomethylpyrrolidine(1,1-cyclobutane-dicarboxylato)-2-plati num(II) monohydrate).

We examined the mechanism of the inhibition of DNA synthesis by a new platinum compound, (-)-(R)-2-aminomethylpyrrolidine(1,1-cyclobutane-dicarboxylato+ ++)-2-platinum(II) monohydrate (DWA-2114R), a derivative of the antitumor drug cis-diamminedichloroplatinum(II) (CDDP), using prokaryotic and eukaryotic DNA polymerases. Preincubating activated DNA with CDDP or DWA-2114R reduced its template activity for prokaryotic and eukaryotic DNA polymerases in a dose-dependent manner. DWA2114R required six times greater drug concentration and two times longer incubation time to show the same decrease of the template activity compared to CDDP. Treatment of primed pUC118 ssDNA templates with the two drugs followed by second-strand synthesis by prokaryotic and eukaryotic DNA polymerases revealed that DWA2114R bound to DNA in a similar manner to CDDP and these adducts blocked DNA elongation by DNA polymerases of eukaryotes as well as of prokaryotes. With these two drugs, the elongations by E. coli DNA polymerase I (Klenow fragment), T7 DNA polymerase and calf thymus DNA polymerase alpha were strongly arrested at guanine-guanine sequences (GG). Stop bands were also observed at adenine-guanine sequences (AG) guanine-adenine-guanine sequences (GAG) and mono-guanine sequence (G). Calf testis DNA polymerase beta was also arrested efficiently at AG, GAG and G, but much more weakly at GG. This pattern was common to DWA2114R and CDDP.

Animals↗
PubMed1991

Mechanisms of inhibitions of DNA polymerase gamma by nucleotide analogues having anti-HIV activities.

Inhibition mechanisms of 5'-triphosphates of 3'-azido-3'-deoxythymidine (AZT-TP) and 3'-deoxythymidine (ddTTP) on extensively purified DNA polymerase gamma from bovine testes were examined by analysis of the products synthesized on singly primed M13mp18 single-stranded DNA or synthetic oligonucleotide template-primer in the presence of analogues. The results indicate that AZT-TP inhibits DNA polymerase gamma in competition with dTTP but is not incorporated into DNA, whereas ddTTP is incorporated into DNA and causes chain termination.

Animals↗
PubMed1989

1-beta-D-arabinofuranosyl-5-(E)-(4-azidostyryl)-uracil 5'-triphosphate: synthesis and utilization as a photoaffinity labeling reagent for DNA polymerase alpha from cherry salmon, Oncorhynchus masou.

For developing a photoaffinity labeling reagent for DNA polymerase alpha, we synthesized 1-beta-D-arabinofuranosyl-5-(4-azidostyryl)-uracil 5'-triphosphate [5-(E)-(4-azidostyryl)-araUTP] bearing a photoreactive aryl azido group. This compound was easily decomposed by photolysis by light above 300 nm. This analogue strongly inhibited DNA polymerase alpha purified from cherry salmon, Oncorhynchus masou, testes; the mode of inhibition was mixed when the enzyme reaction was carried out under room light, and was competitive to dTTP in the dark. From the results of photoaffinity labeling experiments using an analogue containing [gamma-32P], it appeared that this analogue could bind to dTTP binding site of DNA polymerase alpha. Thus, this compound should be very useful for analysis of nucleotide binding sites of this enzyme.

Affinity Labels↗
PubMed1989

Rapid purification and structural study of DNA topoisomerase I from human Burkitt lymphoma Raji cells.

We have developed a rapid purification method for DNA topoisomerase I from Raji cells, a human Burkitt lymphoma cell line, using ammonium sulfate fractionation followed by chromatography on a Mono S column (FPLC, Pharmacia). By this method, the enzyme could be purified to near homogeneity within one day. Electrophoresis on sodium dodecyl sulfate polyacrylamide gel revealed that the final preparation is mainly composed of a 100-kDa protein. The major enzyme activity sedimented through a glycerol density gradient at 5.7S, accompanied with a minor peak at 8.7S. The former may correspond to the monomer of the 100-kDa polypeptide, and the latter, to its dimeric form. The gel filtration study of the crude extract revealed an active molecular species of 200 kDa, in addition to 100 kDa, and lower molecular weight forms. These results suggest that DNA topoisomerase I is largely in monomeric form, but also has a minor population of the dimeric form.

Burkitt Lymphoma↗
PubMed1989

Kynurenine metabolism and xanthurenic acid formation in vitamin B6-deficient rat after tryptophan injection.

Normal and vitamin B6-deficient rats received an intraperitoneal injection of 30 mg/100g of body wt, and the contents of metabolites in kidney or plasma and the related enzyme activities in kidney were determined. The contents of kynurenine and 3-hydroxykynurenine in B6-deficient rat plasma and kidney were much higher than those in normal rat. The changes of those contents in plasma were parallel to those in kidney, but not in liver. The contents of kynurenic acid and xanthurenic acid in B6-deficient liver, plasma, and kidney were also much higher than those in normal rats. However, the changes of those contents in plasma were parallel to those in liver, but not in kidney. Xanthurenic acid and kynurenic acid accumulated to a much greater extent in kidney than in plasma and liver. Kidney kynureninase activity was very low, but kynurenine aminotransferase activities were very high. These observations indicated that the production of xanthurenic acid after tryptophan injection was favorable in B6-deficient kidney with respect to enzyme activities and substrate concentrations, and suggested that kidney took up kynurenine or 3-hydroxykynurenine from blood and after conversion of them it excreted xanthurenic or kynurenic acid into urine.

Animals↗
PubMed1989

Sequence specificity of the human autonomously replicating sequence binding protein.

We have previously found that the protein which bound to the essential region of human autonomously replicating sequences (ARS) could be the c-myc proto-oncogene product. Here we examined the binding specificity of human ARS binding protein purified from Burkitt's lymphoma Raji cells. Among several oligodeoxynucleotides, this protein bound to the fragments containing the sequence of 5'-CAPyCTCTNA-3'. Competition analysis revealed that the ARS binding protein could recognize not only the nucleotide sequences but also the high ordered structure.

Base Sequence↗
PubMed1988

AraUTP-Affi-Gel 10: a novel affinity absorbent for the specific purification of DNA polymerase alpha-primase.

For the specific purification of eukaryotic DNA-dependent DNA polymerase alpha, we prepared two novel affinity resins bearing 5-(E)-(4-aminostyryl) araUTP as a ligand. One of them was araUTP-Sepharose 4B which was coupled directly with the ligand and the other was araUTP-Affi-Gel 10 which was coupled with the ligand through a spacer. No DNA polymerase alpha-primase activity from cherry salmon (Oncorhynchus masou) testes was bound on the araUTP-Sepharose 4B in all cases examined. On the other hand, the araUTP-Affi-Gel 10 retains this enzyme activity when poly(dA) or poly(dA)-oligo(dT)12-18 is present. The retained enzyme activity was sharply eluted around 100-mM KCl concentrations as a single peak, and this fraction showed a specific activity of about 170,000 units/mg as alpha-polymerase activity. The highly purified DNA polymerase alpha-primase isolated using the araUTP-Affi-Gel 10 contained only three polypeptides, which showed Mr values of 120,000, 62,000, and 58,000, respectively, as judged using sodium dodecyl sulfate-polyacrylamide gel electrophoresis.

Animals↗
PubMed1987

Inhibitory effects of 5-alkyl- and 5-alkenyl-1-beta-D-arabinofuranosyluracil 5'-triphosphates on herpes virus-induced DNA polymerases.

Various 5-substituted 1-beta-D-arabinofuranosyluracil 5'-triphosphates (H, methyl, ethyl, n-propyl, n-butyl, (E)-bromovinyl, styryl, and beta-phenylethyl derivatives) were prepared and their inhibitory effects on two different herpes virus-induced DNA polymerases (OMV and HCMV) were studied. These dTTP analogues inhibited the incorporation of [3H]dTMP into DNA in vitro. Among them, analogues having a vinyl group at the 5-position were strongly active against DNA polymerases induced on herpes virus infection. Kinetic analysis showed that the inhibition by the analogues was essentially competitive with respect to the substrate, dTTP. The K1 values (microM) for AraUTP (2.4), AraTTP (1.0), BVAUTP (0.8), and StUAUTP (0.8) were smaller than the Km value (microM) for dTTP (3.4), but those for AraEtUTP, AraPrUTP, and AraBuUTP (5-14) were larger than the Km for dTTP in the case of HCMV-induced DNA polymerase. In contrast to these results, OMV-induced DNA polymerase seemed to be more resistant to these inhibitors than HCMV-induced DNA polymerase. However, the mode of the structure of substituent groups at the 5-position of base moieties is almost the same for the two DNA polymerases, except for in the case of AraUTP itself.

Antiviral Agents↗