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Takemura M. Biochemical properties of the stimulatory activity of DNA polymerase alpha by the hyper-phosphorylated retinoblastoma protein. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1571:151-6. [PMID: 12049795 DOI: 10.1016/s0304-4165(02)00211-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Previously, my colleagues and I have reported that the immunopurified hyper-phosphorylated retinoblastoma protein (ppRb) stimulates the activity of DNA polymerase alpha. I describe here the biochemical characteristics of this stimulatory activity. DNA polymerase alpha-stimulatory activity of ppRb was most remarkable when using activated DNA as a template-primer, rather than using poly(dT)-(rA)(10), poly(dA)-(dT)(12-18), and so on. Kinetic analysis showed that there was no significant difference in K(m) value for deoxyribonucleotides of DNA polymerase alpha in the presence of ppRb. Adding ppRb resulted in the overcoming pause site on the template, but did not affect the rate of misincorporation of incorrect deoxyribonucleotides. By adding ppRb, the optimal concentration of template-primer was shifted to a higher region, but not using M13 singly primed DNA. The ppRb seemed to assist the process that DNA polymerase alpha changed its conformation resulting in appropriate enzyme activity. These results suggest that ppRb affects both template-primer and DNA polymerase alpha and makes appropriate circumstances for the enzyme reaction.
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Affiliation(s)
- Masaharu Takemura
- Laboratory of Cancer Cell Biology, Research Institute for Disease Mechanism and Control, Nagoya University Graduate School of Medicine, Tsurumai-cho 65, Showa-ku, Japan.
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2
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Simbulan C, Suzuki M, Izuta S, Sakurai T, Savoysky E, Kojima K, Miyahara K, Shizuta Y, Yoshida S. Poly(ADP-ribose) polymerase stimulates DNA polymerase alpha by physical association. J Biol Chem 1993. [DOI: 10.1016/s0021-9258(18)54119-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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3
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Mesner LD, Hockensmith JW. Probing the energetics of oligo(dT).poly(dA) by laser cross-linking. Proc Natl Acad Sci U S A 1992; 89:2521-5. [PMID: 1557354 PMCID: PMC48693 DOI: 10.1073/pnas.89.7.2521] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Experimentally determined changes in free energy (delta G(o)) for thymine-thymine interactions occurring in oligo(dT).poly(dA) are dependent on the method used for preparation of the double-stranded template. A rapid laser cross-linking technique was used to examine the equilibrium between oligomers of (dT) bound to either poly(dA) or poly(rA). The single-pulse (4-6 nsec) ultraviolet laser excitation of these polynucleotides causes pyrimidine dimer formation between contiguous oligo(dT) molecules, resulting in a "ligation" of the oligomers. Analysis of the resulting data using standard binding isotherms allowed determination of the degree of cooperativity existing between oligomers. Using the cooperativity, delta G(o), delta H(o), and delta S(o) are calculated, thereby providing thermodynamic parameters for this interaction. The measured cooperativity of oligo(dT) molecule interactions allows direct calculation of the number of 3' ends available as nicked structures or the number of 3' ends associated with gaps for oligo(dT).poly(dA) when used as a substrate for DNA synthesis.
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Affiliation(s)
- L D Mesner
- Department of Biochemistry, University of Virginia Health Sciences Center, Charlottesville 22908
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4
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Goulian M, Heard CJ, Grimm SL. Purification and properties of an accessory protein for DNA polymerase alpha/primase. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(19)38288-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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5
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Masutani C, Enomoto T, Suzuki M, Hanaoka F, Ui M. DNA primase stimulatory factor from mouse FM3A cells has an RNase H activity. Purification of the factor and analysis of the stimulation. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(18)86932-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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6
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Seki M, Enomoto T, Eki T, Miyajima A, Murakami Y, Hanaoka F, Ui M. DNA helicase and nucleoside-5'-triphosphatase activities of polyoma virus large tumor antigen. Biochemistry 1990; 29:1003-9. [PMID: 2160269 DOI: 10.1021/bi00456a024] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Polyoma virus large tumor antigen (PyV T antigen) has been purified to near homogeneity by immunoaffinity column chromatography. We have detected DNA helicase and ATPase (nucleoside-5'-triphosphatase) activities in the purified PyV T antigen fraction and characterized these activities. The ATPase activity was stimulated about 2-fold by poly(dT), which was the most effective stimulator among the synthetic polynucleotides tested. Natural nucleic acids, such as calf thymus native and heat-denatured DNA, and single-stranded circular fd DNA were also effective, but the degree of stimulation was less than 1.5-fold. The basal and poly(dT)-stimulated ATPase activities showed similar preference for nucleoside 5'-triphosphates, requirement for divalent cations, and pH optima. The preference for nucleoside 5'-triphosphates was ATP, dATP greater than CTP, UTP much greater than GTP. The only difference observed between the two activities was salt sensitivity. The basal ATPase activity was resistant to KC1 up to 300 mM. In contrast, poly-(dT)-stimulated activity was reduced to the level of basal activity at 300 mM KC1. DNA helicase activity required divalent cations and was dependent on hydrolysis of ATP. The activity showed similar preference for nucleoside 5'-triphosphates, requirement for divalent cations, and pH optimum as the two ATPase activities, and the salt sensitivity of DNA helicase activity was similar to that of poly(dT)-stimulated ATPase activity. The helicase activity was inhibited competitively by the addition of single-stranded or double-stranded DNA, and a relatively high inhibitory activity was observed with poly [d(A-T)]. The PyV T antigen helicase was found to migrate in the 3' to 5' direction along the DNA strand to which the protein bound.
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Affiliation(s)
- M Seki
- Department of Physiological Chemistry, Faculty of Pharmaceutical Sciences, University of Tokyo, Japan
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7
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Orlando P, Geremia R, Frusciante C, Grippo P. Replicating premeiotic germ cells of the mouse contain a novel DNA primase stimulatory factor. CELL DIFFERENTIATION AND DEVELOPMENT : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF DEVELOPMENTAL BIOLOGISTS 1989; 27:129-36. [PMID: 2766046 DOI: 10.1016/0922-3371(89)90742-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A protein factor that stimulates DNA primase activity associated with DNA polymerase alpha has been identified in mouse germ cell populations enriched in spermatogonia and preleptotene spermatocytes. The partially purified factor enhances DNA primase activity from homologous cell types as well as DNA primase activity from Xenopus laevis oocytes in a poly dT or M 13 directed reaction. The factor does not stimulate DNA polymerase alpha activity in a gapped salmon sperm or poly dT-rA directed reaction. The DNA primase stimulating factor is identified in a male mouse germ cell population enriched in premeiotic cells; it is not detectable in middle-late pachytene spermatocytes, spermatids, Sertoli cells or fibroblasts.
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Affiliation(s)
- P Orlando
- Institute of Protein Biochemistry and Enzymology, Naples, Italy
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8
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Suzuki M, Enomoto T, Masutani C, Hanaoka F, Yamada M, Ui M. DNA primase-DNA polymerase α assembly from mouse FM3A cells. J Biol Chem 1989. [DOI: 10.1016/s0021-9258(18)81767-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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9
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Spadari S, Montecucco A, Pedrali-Noy G, Ciarrocchi G, Focher F, Hübscher U. A double-loop model for the replication of eukaryotic DNA. Mutat Res 1989; 219:147-56. [PMID: 2739671 DOI: 10.1016/0921-8734(89)90009-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Coordinated DNA synthesis of both strands at the replication fork by a fixed 'replisome' may cause dynamic and topological problems. Based upon known properties of DNA helicase, DNA primase and DNA topoisomerases, and on novel properties of DNA polymerases and DNA ligase, we propose a 'double-loop' model for the replication of eukaryotic DNA that could minimize such problems.
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Affiliation(s)
- S Spadari
- Istituto di Genetica Biochimica ed Evoluzionistica, CNR, Pavia, Italy
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Kaguni LS, Lehman IR. Eukaryotic DNA polymerase-primase: structure, mechanism and function. BIOCHIMICA ET BIOPHYSICA ACTA 1988; 950:87-101. [PMID: 3289619 DOI: 10.1016/0167-4781(88)90001-2] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- L S Kaguni
- Department of Biochemistry, Michigan State University, East Lansing
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Itaya A, Hironaka T, Tanaka Y, Yoshihara K, Kamiya T. Purification and properties of a specific primase-stimulating factor of bovine thymus. EUROPEAN JOURNAL OF BIOCHEMISTRY 1988; 174:261-6. [PMID: 2838271 DOI: 10.1111/j.1432-1033.1988.tb14092.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The DNA replicase activity of the complex between bovine thymus DNA polymerase alpha and RNA primase was markedly decreased after the purification by ssDNA-cellulose column chromatography. In an attempt to restore the activity by supplementing some fractions eliminated from the purified enzyme, we found that a fraction eluted from the column by increasing salt concentration and 30% ammonium sulfate precipitates of the phosphocellulose-step enzyme possessed a high ability to restore the replicase activity. Thus, the factors were purified to near homogeneity from the two sources and the properties were examined. Both factors were heat-labile and trypsin-sensitive, possessed a native molecular mass of approximately 150-200 kDa as judged by Sephacryl S-200 column chromatography, and were composed of two polypeptides of 146 kDa and 47 kDa on SDS/polyacrylamide gel electrophoresis, indicating that they were an identical protein. The factor, which did not show any DNA polymerase or primase activities by itself, stimulated approximately 20-fold the replicase activity of purified DNA-polymerase-alpha-primase at a very low concentration (10 ng/50 microliter). The factor did not affect the deoxyribonucleotide polymerizing activity of the enzyme complex at all, but specifically stimulated the primase activity only. Thus, we designated the factor as primase-stimulating factor. Although varying the template concentration did not significantly affect the mode of stimulation, increasing the concentration of substrate for primer synthesis (ATP) markedly decreased the extent of stimulation. Thus, the stimulating factor seems to decrease the substrate concentration required for the primase reaction as well as increasing threefold the maximum activity attained by varying the substrate concentration. So far, no ATPase activity has been detected in the factor.
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Affiliation(s)
- A Itaya
- Department of Biochemistry, Nara Medical University, Japan
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13
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Eki T, Enomoto T, Murakami Y, Hanaoka F, Yamada M. Characterization of DNA polymerase alpha activity from a mouse DNA temperature-sensitive mutant, strain tsFT20, which shows a defect in DNA polymerase alpha activity at restrictive temperatures. Arch Biochem Biophys 1988; 260:552-60. [PMID: 3341757 DOI: 10.1016/0003-9861(88)90481-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
tsFT20 cells derived from mouse FM3A cells are DNA temperature-sensitive mutants, which have heat-labile DNA polymerase alpha activity. When tsFT20 cells were incubated at restrictive temperatures, intracellular levels of DNA polymerase alpha activity changed biphasically, showing an initial fast decrease (phase I) and a subsequent slow decrease (phase II). The activity of DNA polymerase alpha from tsFT20 cells cultured at a permissive temperature (33 degrees C) was greatly increased by the addition of glycerol or ethylene glycol to the reaction mixture, while little increase in enzyme activity was observed at any concentration of glycerol or ethylene glycol tested with the enzyme from the cells cultured at a restrictive temperature (39 degrees C) for 8 h (phase II). The activity of DNA polymerase alpha from wild-type cells was also increased by the addition of glycerol but the increase was much less than that in the tsFT20 cells. An in vitro preincubation experiment showed that DNA polymerase alpha from tsFT20 cells cultured at 33 degrees C very rapidly lost its ability to be stimulated by glycerol. Furthermore, the experiment using the extracts prepared from tsFT20 cells cultured at 39 degrees C for various periods showed that the ability to be stimulated by glycerol decreased with the duration of incubation time at 39 degrees C. DNA polymerase alpha from the revertants, which can grow at 39 degrees C and exhibit a partial recovery in heat stability of DNA polymerase alpha activity, showed an intermediate response to glycerol, between those of DNA polymerase alpha from tsFT20 and from the wild-type cells. Finally, it was observed that the level of enzyme activity that can be stimulated by glycerol correlated well with the DNA synthesizing ability of tsFT20 cells.
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Affiliation(s)
- T Eki
- Department of Physiological Chemistry, Faculty of Pharmaceutical Sciences, University of Tokyo, Japan
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Ottiger H, Frei P, Hässig M, Hübscher U. Mammalian DNA polymerase alpha: a replication competent holoenzyme form from calf thymus. Nucleic Acids Res 1987; 15:4789-807. [PMID: 3601656 PMCID: PMC305918 DOI: 10.1093/nar/15.12.4789] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
A complex "replication competent" holoenzyme form of DNA polymerase alpha (RC-alpha) was purified 10,000 fold from calf thymus through the use of an assay employing primed single stranded circular DNA template. The RC-alpha form could partially replicate a double-stranded oligo(dT)-tailed linear DNA and could completely convert primed single-stranded circular DNA to its double stranded form. The RC-alpha was resolved by denaturing gel electrophoresis into at least 10 discrete polypeptide species ranging in apparent molecular mass from 200 to 47 kilodaltons; three of the bands (apparent Mr of 200, 118 and 63 kilodaltons) displayed DNA polymerase activity in denaturing gel activity assay. The isolation of RC-alpha required the use of absolutely fresh calf thymus, the inclusion of ATP and protease inhibitors throughout the purification procedure. Treatment of the RC-alpha with the neutralizing anti-DNA polymerase alpha monoclonal antibody SJK 132-20 (Tanaka et al. (1982), J. Biol. Chem. 257, 8386-8390) in nondenaturing conditions selected the complete set of 10 polypeptides, whereas treatment in denaturing conditions selected the 200 kilodalton catalytic DNA polymerase active polypeptide. The properties and the behaviour of the RC-alpha preparation following removal of specific polypeptides strongly suggested that the capacity of RC-alpha to extend and replicate long template requires the function of nonproteolysed form of the 200 kilodaltons catalytic DNA polymerase core and at least 6 other auxiliary polypeptides of, respectively, 98, 87, 63, 54, 49 and 47 kilodaltons.
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