Journal articles: 'DNA Polymerase III'

1

Glover, Bradley P., and Charles S. McHenry. "The DNA Polymerase III Holoenzyme." Cell 105, no. 7 (June 2001): 925–34. http://dx.doi.org/10.1016/s0092-8674(01)00400-7.

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2

Maslowska, Katarzyna H., Karolina Makiela-Dzbenska, Jin-Yao Mo, Iwona J. Fijalkowska, and Roel M. Schaaper. "High-accuracy lagging-strand DNA replication mediated by DNA polymerase dissociation." Proceedings of the National Academy of Sciences 115, no. 16 (April 2, 2018): 4212–17. http://dx.doi.org/10.1073/pnas.1720353115.

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The fidelity of DNA replication is a critical factor in the rate at which cells incur mutations. Due to the antiparallel orientation of the two chromosomal DNA strands, one strand (leading strand) is replicated in a mostly processive manner, while the other (lagging strand) is synthesized in short sections called Okazaki fragments. A fundamental question that remains to be answered is whether the two strands are copied with the same intrinsic fidelity. In most experimental systems, this question is difficult to answer, as the replication complex contains a different DNA polymerase for each strand, such as, for example, DNA polymerases δ and ε in eukaryotes. Here we have investigated this question in the bacterium Escherichia coli, in which the replicase (DNA polymerase III holoenzyme) contains two copies of the same polymerase (Pol III, the dnaE gene product), and hence the two strands are copied by the same polymerase. Our in vivo mutagenesis data indicate that the two DNA strands are not copied with the same accuracy, and that, remarkably, the lagging strand has the highest fidelity. We postulate that this effect results from the greater dissociative character of the lagging-strand polymerase, which provides additional options for error removal. Our conclusion is strongly supported by results with dnaE antimutator polymerases characterized by increased dissociation rates.

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3

Budd, M. E., K. D. Wittrup, J. E. Bailey, and J. L. Campbell. "DNA polymerase I is required for premeiotic DNA replication and sporulation but not for X-ray repair in Saccharomyces cerevisiae." Molecular and Cellular Biology 9, no. 2 (February 1989): 365–76. http://dx.doi.org/10.1128/mcb.9.2.365-376.1989.

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We have used a set of seven temperature-sensitive mutants in the DNA polymerase I gene of Saccharomyces cerevisiae to investigate the role of DNA polymerase I in various aspects of DNA synthesis in vivo. Previously, we showed that DNA polymerase I is required for mitotic DNA replication. Here we extend our studies to several stages of meiosis and repair of X-ray-induced damage. We find that sporulation is blocked in all of the DNA polymerase temperature-sensitive mutants and that premeiotic DNA replication does not occur. Commitment to meiotic recombination is only 2% of wild-type levels. Thus, DNA polymerase I is essential for these steps. However, repair of X-ray-induced single-strand breaks is not defective in the DNA polymerase temperature-sensitive mutants, and DNA polymerase I is therefore not essential for repair of such lesions. These results suggest that DNA polymerase II or III or both, the two other nuclear yeast DNA polymerases for which roles have not yet been established, carry out repair in the absence of DNA polymerase I, but that DNA polymerase II and III cannot compensate for loss of DNA polymerase I in meiotic replication and recombination. These results do not, however, rule out essential roles for DNA polymerase II or III or both in addition to that for DNA polymerase I.

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4

Budd, M. E., K. D. Wittrup, J. E. Bailey, and J. L. Campbell. "DNA polymerase I is required for premeiotic DNA replication and sporulation but not for X-ray repair in Saccharomyces cerevisiae." Molecular and Cellular Biology 9, no. 2 (February 1989): 365–76. http://dx.doi.org/10.1128/mcb.9.2.365.

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We have used a set of seven temperature-sensitive mutants in the DNA polymerase I gene of Saccharomyces cerevisiae to investigate the role of DNA polymerase I in various aspects of DNA synthesis in vivo. Previously, we showed that DNA polymerase I is required for mitotic DNA replication. Here we extend our studies to several stages of meiosis and repair of X-ray-induced damage. We find that sporulation is blocked in all of the DNA polymerase temperature-sensitive mutants and that premeiotic DNA replication does not occur. Commitment to meiotic recombination is only 2% of wild-type levels. Thus, DNA polymerase I is essential for these steps. However, repair of X-ray-induced single-strand breaks is not defective in the DNA polymerase temperature-sensitive mutants, and DNA polymerase I is therefore not essential for repair of such lesions. These results suggest that DNA polymerase II or III or both, the two other nuclear yeast DNA polymerases for which roles have not yet been established, carry out repair in the absence of DNA polymerase I, but that DNA polymerase II and III cannot compensate for loss of DNA polymerase I in meiotic replication and recombination. These results do not, however, rule out essential roles for DNA polymerase II or III or both in addition to that for DNA polymerase I.

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5

Bonner, C. A., P. T. Stukenberg, M. Rajagopalan, R. Eritja, M. O'Donnell, K. McEntee, H. Echols, and M. F. Goodman. "Processive DNA synthesis by DNA polymerase II mediated by DNA polymerase III accessory proteins." Journal of Biological Chemistry 267, no. 16 (June 1992): 11431–38. http://dx.doi.org/10.1016/s0021-9258(19)49928-6.

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6

Bryan, Sharon K., Michael Hagensee, and Robb E. Moses. "Holoenzyme DNA polymerase III fixes mutations." Mutation Research Letters 243, no. 4 (April 1990): 313–18. http://dx.doi.org/10.1016/0165-7992(90)90149-e.

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7

Pritchard, Arthur E., and Charles S. McHenry. "Assembly of DNA Polymerase III Holoenzyme." Journal of Biological Chemistry 276, no. 37 (July 19, 2001): 35217–22. http://dx.doi.org/10.1074/jbc.m102735200.

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8

Fijalkowska, I. J., and R. M. Schaaper. "Antimutator mutations in the alpha subunit of Escherichia coli DNA polymerase III: identification of the responsible mutations and alignment with other DNA polymerases." Genetics 134, no. 4 (August 1, 1993): 1039–44. http://dx.doi.org/10.1093/genetics/134.4.1039.

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Abstract The dnaE gene of Escherichia coli encodes the DNA polymerase (alpha subunit) of the main replicative enzyme, DNA polymerase III holoenzyme. We have previously identified this gene as the site of a series of seven antimutator mutations that specifically decrease the level of DNA replication errors. Here we report the nucleotide sequence changes in each of the different antimutator dnaE alleles. For each a single, but different, amino acid substitution was found among the 1,160 amino acids of the protein. The observed substitutions are generally nonconservative. All affected residues are located in the central one-third of the protein. Some insight into the function of the regions of polymerase III containing the affected residues was obtained by amino acid alignment with other DNA polymerases. We followed the principles developed in 1990 by M. Delarue et al. who have identified in DNA polymerases from a large number of prokaryotic and eukaryotic sources three highly conserved sequence motifs, which are suggested to contain components of the polymerase active site. We succeeded in finding these three conserved motifs in polymerase III as well. However, none of the amino acid substitutions responsible for the antimutator phenotype occurred at these sites. This and other observations suggest that the effect of these mutations may be exerted indirectly through effects on polymerase conformation and/or DNA/polymerase interactions.

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9

LOGAN, KELLEY, and STEVEN ACKERMAN. "Effects of Antibiotics on RNA Polymerase III Transcription." DNA 7, no. 7 (September 1988): 483–91. http://dx.doi.org/10.1089/dna.1.1988.7.483.

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10

De, Ananya, and Colin Campbell. "A novel interaction between DNA ligase III and DNA polymerase γ plays an essential role in mitochondrial DNA stability." Biochemical Journal 402, no. 1 (January 25, 2007): 175–86. http://dx.doi.org/10.1042/bj20061004.

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The data in the present study show that DNA polymerase γ and DNA ligase III interact in mitochondrial protein extracts from cultured HT1080 cells. An interaction was also observed between the two recombinant proteins in vitro. Expression of catalytically inert versions of DNA ligase III that bind DNA polymerase γ was associated with reduced mitochondrial DNA copy number and integrity. In contrast, overexpression of wild-type DNA ligase III had no effect on mitochondrial DNA copy number or integrity. Experiments revealed that wild-type DNA ligase III facilitates the interaction of DNA polymerase γ with a nicked DNA substrate in vitro, and that the zinc finger domain of DNA ligase III is required for this activity. Mitochondrial protein extracts prepared from cells overexpressing a DNA ligase III protein that lacked the zinc finger domain had reduced base excision repair activity compared with extracts from cells overexpressing the wild-type protein. These data support the interpretation that the interaction of DNA ligase III and DNA polymerase γ is required for proper maintenance of the mammalian mitochondrial genome.

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11

Studwell-Vaughan, P. S., and M. O'Donnell. "Constitution of the twin polymerase of DNA polymerase III holoenzyme." Journal of Biological Chemistry 266, no. 29 (October 1991): 19833–41. http://dx.doi.org/10.1016/s0021-9258(18)55067-5.

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12

McHenry, Charles S. "DNA Polymerase III Holoenzyme of Escherichia coli." Annual Review of Biochemistry 57, no. 1 (June 1988): 519–50. http://dx.doi.org/10.1146/annurev.bi.57.070188.002511.

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13

Kim, Deok Ryong, and Charles S. McHenry. "In VivoAssembly of Overproduced DNA Polymerase III." Journal of Biological Chemistry 271, no. 34 (August 23, 1996): 20681–89. http://dx.doi.org/10.1074/jbc.271.34.20681.

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14

Sanjanwala, B., and A. T. Ganesan. "DNA polymerase III gene of Bacillus subtilis." Proceedings of the National Academy of Sciences 86, no. 12 (June 1, 1989): 4421–24. http://dx.doi.org/10.1073/pnas.86.12.4421.

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15

Hughes, A. J., S. K. Bryan, H. Chen, R. E. Moses, and C. S. McHenry. "Escherichia coli DNA polymerase II is stimulated by DNA polymerase III holoenzyme auxiliary subunits." Journal of Biological Chemistry 266, no. 7 (March 1991): 4568–73. http://dx.doi.org/10.1016/s0021-9258(20)64360-5.

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16

Maki, S., and A. Kornberg. "DNA polymerase III holoenzyme of Escherichia coli. III. Distinctive processive polymerases reconstituted from purified subunits." Journal of Biological Chemistry 263, no. 14 (May 1988): 6561–69. http://dx.doi.org/10.1016/s0021-9258(18)68678-8.

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17

O'Donnell, M., J. Kuriyan, X. P. Kong, P. T. Stukenberg, and R. Onrust. "The sliding clamp of DNA polymerase III holoenzyme encircles DNA." Molecular Biology of the Cell 3, no. 9 (September 1992): 953–57. http://dx.doi.org/10.1091/mbc.3.9.953.

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18

Bailey, Scott, Richard A. Wing, and Thomas A. Steitz. "The Structure of T. aquaticus DNA Polymerase III Is Distinct from Eukaryotic Replicative DNA Polymerases." Cell 126, no. 5 (September 2006): 893–904. http://dx.doi.org/10.1016/j.cell.2006.07.027.

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19

Burgers, Peter M. J. "Mammalian cyclin/PCNA (DNA polymerase δ auxiliary protein) stimulates processive DNA synthesis by yeast DNA polymerase III." Nucleic Acids Research 16, no. 14 (1988): 6297–307. http://dx.doi.org/10.1093/nar/16.14.6297.

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20

Ribble, Wendy, Shawn D. Kane, and James M. Bullard. "Long-Range PCR Amplification of DNA by DNA Polymerase III Holoenzyme from Thermus thermophilus." Enzyme Research 2015 (January 19, 2015): 1–16. http://dx.doi.org/10.1155/2015/837842.

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DNA replication in bacteria is accomplished by a multicomponent replicase, the DNA polymerase III holoenzyme (pol III HE). The three essential components of the pol III HE are the α polymerase, the β sliding clamp processivity factor, and the DnaX clamp-loader complex. We report here the assembly of the functional holoenzyme from Thermus thermophilus (Tth), an extreme thermophile. The minimal holoenzyme capable of DNA synthesis consists of α, β and DnaX (τ and γ), δ and δ′ components of the clamp-loader complex. The proteins were each cloned and expressed in a native form. Each component of the system was purified extensively. The minimum holoenzyme from these five purified subunits reassembled is sufficient for rapid and processive DNA synthesis. In an isolated form the α polymerase was found to be unstable at temperatures above 65°C. We were able to increase the thermostability of the pol III HE to 98°C by addition and optimization of various buffers and cosolvents. In the optimized buffer system we show that a replicative polymerase apparatus, Tth pol III HE, is capable of rapid amplification of regions of DNA up to 15,000 base pairs in PCR reactions.

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21

Campbell, F. E., and D. R. Setzer. "Transcription termination by RNA polymerase III: uncoupling of polymerase release from termination signal recognition." Molecular and Cellular Biology 12, no. 5 (May 1992): 2260–72. http://dx.doi.org/10.1128/mcb.12.5.2260-2272.1992.

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Xenopus RNA polymerase III specifically initiates transcription on poly(dC)-tailed DNA templates in the absence of other class III transcription factors normally required for transcription initiation. In experimental analyses of transcription termination using DNA fragments with a 5S rRNA gene positioned downstream of the tailed end, only 40% of the transcribing polymerase molecules terminate at the normally efficient Xenopus borealis somatic-type 5S rRNA terminators; the remaining 60% read through these signals and give rise to runoff transcripts. We find that the nascent RNA strand is inefficiently displaced from the DNA template during transcription elongation. Interestingly, only polymerases synthesizing a displaced RNA terminate at the 5S rRNA gene terminators; when the nascent RNA is not displaced from the template, read-through transcripts are synthesized. RNAs with 3' ends at the 5S rRNA gene terminators are judged to result from authentic termination events on the basis of multiple criteria, including kinetic properties, the precise 3' ends generated, release of transcripts from the template, and recycling of the polymerase. Even though only 40% of the polymerase molecules ultimately terminate at either of the tandem 5S rRNA gene terminators, virtually all polymerases pause there, demonstrating that termination signal recognition can be experimentally uncoupled from polymerase release. Thus, termination is dependent on RNA strand displacement during transcription elongation, whereas termination signal recognition is not. We interpret our results in terms of a two-step model for transcription termination in which polymerase release is dependent on the fate of the nascent RNA strand during transcription elongation.

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22

Campbell, F. E., and D. R. Setzer. "Transcription termination by RNA polymerase III: uncoupling of polymerase release from termination signal recognition." Molecular and Cellular Biology 12, no. 5 (May 1992): 2260–72. http://dx.doi.org/10.1128/mcb.12.5.2260.

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Xenopus RNA polymerase III specifically initiates transcription on poly(dC)-tailed DNA templates in the absence of other class III transcription factors normally required for transcription initiation. In experimental analyses of transcription termination using DNA fragments with a 5S rRNA gene positioned downstream of the tailed end, only 40% of the transcribing polymerase molecules terminate at the normally efficient Xenopus borealis somatic-type 5S rRNA terminators; the remaining 60% read through these signals and give rise to runoff transcripts. We find that the nascent RNA strand is inefficiently displaced from the DNA template during transcription elongation. Interestingly, only polymerases synthesizing a displaced RNA terminate at the 5S rRNA gene terminators; when the nascent RNA is not displaced from the template, read-through transcripts are synthesized. RNAs with 3' ends at the 5S rRNA gene terminators are judged to result from authentic termination events on the basis of multiple criteria, including kinetic properties, the precise 3' ends generated, release of transcripts from the template, and recycling of the polymerase. Even though only 40% of the polymerase molecules ultimately terminate at either of the tandem 5S rRNA gene terminators, virtually all polymerases pause there, demonstrating that termination signal recognition can be experimentally uncoupled from polymerase release. Thus, termination is dependent on RNA strand displacement during transcription elongation, whereas termination signal recognition is not. We interpret our results in terms of a two-step model for transcription termination in which polymerase release is dependent on the fate of the nascent RNA strand during transcription elongation.

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23

Herendeen, Daniel R., and Thomas J. Kelly. "DNA Polymerase III: Running Rings around the Fork." Cell 84, no. 1 (January 1996): 5–8. http://dx.doi.org/10.1016/s0092-8674(00)80069-0.

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24

Gawel, Damian, Phuong T. Pham, Iwona J. Fijalkowska, Piotr Jonczyk, and Roel M. Schaaper. "Role of Accessory DNA Polymerases in DNA Replication in Escherichia coli: Analysis of the dnaX36 Mutator Mutant." Journal of Bacteriology 190, no. 5 (December 21, 2007): 1730–42. http://dx.doi.org/10.1128/jb.01463-07.

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ABSTRACT The dnaX36(TS) mutant of Escherichia coli confers a distinct mutator phenotype characterized by enhancement of transversion base substitutions and certain (−1) frameshift mutations. Here, we have further investigated the possible mechanism(s) underlying this mutator effect, focusing in particular on the role of the various E. coli DNA polymerases. The dnaX gene encodes the τ subunit of DNA polymerase III (Pol III) holoenzyme, the enzyme responsible for replication of the bacterial chromosome. The dnaX36 defect resides in the C-terminal domain V of τ, essential for interaction of τ with the α (polymerase) subunit, suggesting that the mutator phenotype is caused by an impaired or altered α-τ interaction. We previously proposed that the mutator activity results from aberrant processing of terminal mismatches created by Pol III insertion errors. The present results, including lack of interaction of dnaX36 with mutM, mutY, and recA defects, support our assumption that dnaX36-mediated mutations originate as errors of replication rather than DNA damage-related events. Second, an important role is described for DNA Pol II and Pol IV in preventing and producing, respectively, the mutations. In the system used, a high fraction of the mutations is dependent on the action of Pol IV in a (dinB) gene dosage-dependent manner. However, an even larger but opposing role is deduced for Pol II, revealing Pol II to be a major editor of Pol III mediated replication errors. Overall, the results provide insight into the interplay of the various DNA polymerases, and of τ subunit, in securing a high fidelity of replication.

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25

Bridges, B. A., Helen Bates, and Firdaus Sharif. "Polymerases and UV mutagenesis in Escherichia coli." Genome 31, no. 2 (January 15, 1989): 572–77. http://dx.doi.org/10.1139/g89-106.

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Evidence for and against the involvement of the known nucleic acid polymerases in UV mutagenesis in Escherichia coli is reviewed. There is no evidence that rules out the participation of any of them when they are present but only one, the α subunit of DNA polymerase III holoenzyme (polC gene product) has been shown to be essential. It is argued that the PolC protein that functions in UV mutagenesis may not be immediately recognizable as one of the normal cellular polymerases or polymerase complexes.Key words: polymerases, ultraviolet light, mutagenesis, DNA repair, misincorporation.

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26

Cvekl, Aleš, and Květa Horská. "Cibacron Blue inhibition of prokaryotic and eukaryotic DNA-dependent RNA polymerases." Collection of Czechoslovak Chemical Communications 55, no. 11 (1990): 2769–80. http://dx.doi.org/10.1135/cccc19902769.

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A comparison was drawn between the action of Cibacron Blue F3GA on the enzymic activity of DNA-dependent RNA polymerases from different sources, e.g. Escherichia coli, calf thymus and wheat germ (polymerase II). Sensitivity towards this inhibitor was determined for polymer formation and primed abortive synthesis of trinucleotide UpApU. In case of E. coli polymerase and wheat germ polymerase II the dye inhibits both polymer formation and abortive synthesis. Calf thymus polymerase II is inhibited only in the polymerisation step. The primed initiation reaction was found to be resistant towards the dye. In case of E. coli polymerase and wheat germ polymerase II the sensitive step is the formation of internucleotide bond whereas in case of calf thymus polymerase II the translocation of the enzyme is influenced. An analysis of kinetic data indicates more than one binding site for the dye on RNA polymerase II from calf thymus and wheat germ. Cibacron blue does not inhibit specific transcription catalyzed by RNA polymerase III from human HeLa cells and mouse leukemia L1210 cells.

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27

Suszek, Waldemar, Hanna Baranowska, Jerzy Zuk, and Witold J. Jachymczyk. "DNA polymerase III is required for DNA repair in Saccharomyces cerevisiae." Current Genetics 24, no. 3 (September 1993): 200–204. http://dx.doi.org/10.1007/bf00351792.

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28

Sitney, Karen C., Martin E. Budd, and Judith L. Campbell. "DNA polymerase III, a second essential DNA polymerase, is encoded by the S. cerevisiae CDC2 gene." Cell 56, no. 4 (February 1989): 599–605. http://dx.doi.org/10.1016/0092-8674(89)90582-5.

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29

Thomsen, Darrell R., Nancee L. Oien, Todd A. Hopkins, Mary L. Knechtel, Roger J. Brideau, Michael W. Wathen, and Fred L. Homa. "Amino Acid Changes within Conserved Region III of the Herpes Simplex Virus and Human Cytomegalovirus DNA Polymerases Confer Resistance to 4-Oxo-Dihydroquinolines, a Novel Class of Herpesvirus Antiviral Agents." Journal of Virology 77, no. 3 (February 1, 2003): 1868–76. http://dx.doi.org/10.1128/jvi.77.3.1868-1876.2003.

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ABSTRACT The 4-oxo-dihydroquinolines (PNU-182171 and PNU-183792) are nonnucleoside inhibitors of herpesvirus polymerases (R. J. Brideau et al., Antiviral Res. 54:19-28, 2002; N. L. Oien et al., Antimicrob. Agents Chemother. 46:724-730, 2002). In cell culture these compounds inhibit herpes simplex virus type 1 (HSV-1), HSV-2, human cytomegalovirus (HCMV), varicella-zoster virus (VZV), and human herpesvirus 8 (HHV-8) replication. HSV-1 and HSV-2 mutants resistant to these drugs were isolated and the resistance mutation was mapped to the DNA polymerase gene. Drug resistance correlated with a point mutation in conserved domain III that resulted in a V823A change in the HSV-1 or the equivalent amino acid in the HSV-2 DNA polymerase. Resistance of HCMV was also found to correlate with amino acid changes in conserved domain III (V823A+V824L). V823 is conserved in the DNA polymerases of six (HSV-1, HSV-2, HCMV, VZV, Epstein-Barr virus, and HHV-8) of the eight human herpesviruses; the HHV-6 and HHV-7 polymerases contain an alanine at this amino acid. In vitro polymerase assays demonstrated that HSV-1, HSV-2, HCMV, VZV, and HHV-8 polymerases were inhibited by PNU-183792, whereas the HHV-6 polymerase was not. Changing this amino acid from valine to alanine in the HSV-1, HCMV, and HHV-8 polymerases alters the polymerase activity so that it is less sensitive to drug inhibition. In contrast, changing the equivalent amino acid in the HHV-6 polymerase from alanine to valine alters polymerase activity so that PNU-183792 inhibits this enzyme. The HSV-1, HSV-2, and HCMV drug-resistant mutants were not altered in their susceptibilities to nucleoside analogs; in fact, some of the mutants were hypersensitive to several of the drugs. These results support a mechanism where PNU-183792 inhibits herpesviruses by interacting with a binding determinant on the viral DNA polymerase that is less important for the binding of nucleoside analogs and deoxynucleoside triphosphates.

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30

MOON, IL SOO, and M. O. KRAUSE. "Common RNA Polymerase I, II, and III Upstream Elements in Mouse 7SK Gene Locus Revealed by the Inverse Polymerase Chain Reaction." DNA and Cell Biology 10, no. 1 (January 1991): 23–32. http://dx.doi.org/10.1089/dna.1991.10.23.

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31

Barnes, Marjorie H., Shelley D. Miller, and Neal C. Brown. "DNA Polymerases of Low-GC Gram-Positive Eubacteria: Identification of the Replication-Specific Enzyme Encoded by dnaE." Journal of Bacteriology 184, no. 14 (July 15, 2002): 3834–38. http://dx.doi.org/10.1128/jb.184.14.3834-3838.2002.

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ABSTRACT dnaE, the gene encoding one of the two replication-specific DNA polymerases (Pols) of low-GC-content gram-positive bacteria (E. Dervyn et al., Science 294:1716-1719, 2001; R. Inoue et al., Mol. Genet. Genomics 266:564-571, 2001), was cloned from Bacillus subtilis, a model low-GC gram-positive organism. The gene was overexpressed in Escherichia coli. The purified recombinant product displayed inhibitor responses and physical, catalytic, and antigenic properties indistinguishable from those of the low-GC gram-positive-organism-specific enzyme previously named DNA Pol II after the polB-encoded DNA Pol II of E. coli. Whereas a polB-like gene is absent from low-GC gram-positive genomes and whereas the low-GC gram-positive DNA Pol II strongly conserves a dnaE-like, Pol III primary structure, it is proposed that it be renamed DNA polymerase III E (Pol III E) to accurately reflect its replicative function and its origin from dnaE. It is also proposed that DNA Pol III, the other replication-specific Pol of low-GC gram-positive organisms, be renamed DNA polymerase III C (Pol III C) to denote its origin from polC. By this revised nomenclature, the DNA Pols that are expressed constitutively in low-GC gram-positive bacteria would include DNA Pol I, the dispensable repair enzyme encoded by polA, and the two essential, replication-specific enzymes Pol III C and Pol III E, encoded, respectively, by polC and dnaE.

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32

Burgers, P. M., and G. A. Bauer. "DNA polymerase III from Saccharomyces cerevisiae. II. Inhibitor studies and comparison with DNA polymerases I and II." Journal of Biological Chemistry 263, no. 2 (January 1988): 925–30. http://dx.doi.org/10.1016/s0021-9258(19)35441-9.

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33

Griep, Mark A. "Fluorescence Recovery Assay: A Continuous Assay for Processive DNA Polymerases Applied Specifically to DNA Polymerase III Holoenzyme." Analytical Biochemistry 232, no. 2 (December 1995): 180–89. http://dx.doi.org/10.1006/abio.1995.0005.

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34

Gridasova, Anastasia A., and R. William Henry. "The p53 Tumor Suppressor Protein Represses Human snRNA Gene Transcription by RNA Polymerases II and III Independently of Sequence-Specific DNA Binding." Molecular and Cellular Biology 25, no. 8 (April 15, 2005): 3247–60. http://dx.doi.org/10.1128/mcb.25.8.3247-3260.2005.

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ABSTRACT Human U1 and U6 snRNA genes are transcribed by RNA polymerases II and III, respectively. While the p53 tumor suppressor protein is a general repressor of RNA polymerase III transcription, whether p53 regulates snRNA gene transcription by RNA polymerase II is uncertain. The data presented herein indicate that p53 is an effective repressor of snRNA gene transcription by both polymerases. Both U1 and U6 transcription in vitro is repressed by recombinant p53, and endogenous p53 occupancy at these promoters is stimulated by UV light. In response to UV light, U1 and U6 transcription is strongly repressed. Human U1 genes, but not U6 genes, contain a high-affinity p53 response element located within the core promoter region. Nonetheless, this element is not required for p53 repression and mutant p53 molecules that do not bind DNA can maintain repression, suggesting a reliance on protein interactions for p53 promoter recruitment. Recruitment may be mediated by the general transcription factors TATA-box binding protein and snRNA-activating protein complex, which interact well with p53 and function for both RNA polymerase II and III transcription.

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35

Dohrmann, Paul R., Raul Correa, Ryan L. Frisch, Susan M. Rosenberg, and Charles S. McHenry. "The DNA polymerase III holoenzyme contains γ and is not a trimeric polymerase." Nucleic Acids Research 44, no. 3 (January 18, 2016): 1285–97. http://dx.doi.org/10.1093/nar/gkv1510.

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36

Barnes, Marjorie H., Russell A. Hammond, Christopher C. Kennedy, Susan L. Mack, and Neal C. Brown. "Localization of the exonuclease and polymerase domains of Bacillus subtilis DNA polymerase III." Gene 111, no. 1 (February 1992): 43–49. http://dx.doi.org/10.1016/0378-1119(92)90601-k.

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37

Furukohri, Asako, Myron F. Goodman, and Hisaji Maki. "A Dynamic Polymerase Exchange withEscherichia coliDNA Polymerase IV Replacing DNA Polymerase III on the Sliding Clamp." Journal of Biological Chemistry 283, no. 17 (February 28, 2008): 11260–69. http://dx.doi.org/10.1074/jbc.m709689200.

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38

Neuwald, A. F. "Evolutionary clues to DNA polymerase III clamp structural mechanisms." Nucleic Acids Research 31, no. 15 (August 1, 2003): 4503–16. http://dx.doi.org/10.1093/nar/gkg486.

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39

Zhao, Xiao-Qian, Jian-Fei Hu, and Jun Yu. "Comparative Analysis of Eubacterial DNA Polymerase III Alpha Subunits." Genomics, Proteomics & Bioinformatics 4, no. 4 (2006): 203–11. http://dx.doi.org/10.1016/s1672-0229(07)60001-1.

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40

Hammond, Russell A., and Neal C. Brown. "Overproduction and purification of Bacillus subtilis DNA polymerase III." Protein Expression and Purification 3, no. 1 (February 1992): 65–70. http://dx.doi.org/10.1016/1046-5928(92)90057-4.

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41

LEHTINEN, Duane A., and Fred W. PERRINO. "Dysfunctional proofreading in the Escherichia coli DNA polymerase III core." Biochemical Journal 384, no. 2 (November 23, 2004): 337–48. http://dx.doi.org/10.1042/bj20040660.

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The ε-subunit contains the catalytic site for the 3′→5′ proofreading exonuclease that functions in the DNA pol III (DNA polymerase III) core to edit nucleotides misinserted by the α-subunit DNA pol. A novel mutagenesis strategy was used to identify 23 dnaQ alleles that exhibit a mutator phenotype in vivo. Fourteen of the ε mutants were purified, and these proteins exhibited 3′→5′ exonuclease activities that ranged from 32% to 155% of the activity exhibited by the wild-type ε protein, in contrast with the 2% activity exhibited by purified MutD5 protein. DNA pol III core enzymes constituted with 11 of the 14 ε mutants exhibited an increased error rate during in vitro DNA synthesis using a forward mutation assay. Interactions of the purified ε mutants with the α- and θ-subunits were examined by gel filtration chromatography and exonuclease stimulation assays, and by measuring polymerase/exonuclease ratios to identify the catalytically active ε511 (I170T/V215A) mutant with dysfunctional proofreading in the DNA pol III core. The ε511 mutant associated tightly with the α-subunit, but the exonuclease activity of ε511 was not stimulated in the α–ε511 complex. Addition of the θ-subunit to generate the α–ε511–θ DNA pol III core partially restored stimulation of the ε511 exonuclease, indicating a role for the θ-subunit in co-ordinating the α–ε polymerase–exonuclease interaction. The α–ε511–θ DNA pol III core exhibited a 3.5-fold higher polymerase/exonuclease ratio relative to the wild-type DNA pol III core, further indicating dysfunctional proofreading in the α–ε511–θ complex. Thus the ε511 mutant has wild-type 3′→5′ exonuclease activity and associates physically with the α- and θ-subunits to generate a proofreading-defective DNA pol III enzyme.

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42

Wrzesiński, Michał, Anetta Nowosielska, Jadwiga Nieminuszczy, and Elzbieta Grzesiuk. "Effect of SOS-induced Pol II, Pol IV, and Pol V DNA polymerases on UV-induced mutagenesis and MFD repair in Escherichia coli cells." Acta Biochimica Polonica 52, no. 1 (March 31, 2005): 139–47. http://dx.doi.org/10.18388/abp.2005_3499.

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Irradiation of organisms with UV light produces genotoxic and mutagenic lesions in DNA. Replication through these lesions (translesion DNA synthesis, TSL) in Escherichia coli requires polymerase V (Pol V) and polymerase III (Pol III) holoenzyme. However, some evidence indicates that in the absence of Pol V, and with Pol III inactivated in its proofreading activity by the mutD5 mutation, efficient TSL takes place. The aim of this work was to estimate the involvement of SOS-inducible DNA polymerases, Pol II, Pol IV and Pol V, in UV mutagenesis and in mutation frequency decline (MFD), a mechanism of repair of UV-induced damage to DNA under conditions of arrested protein synthesis. Using the argE3-->Arg(+) reversion to prototrophy system in E. coli AB1157, we found that the umuDC-encoded Pol V is the only SOS-inducible polymerase required for UV mutagenesis, since in its absence the level of Arg(+) revertants is extremely low and independent of Pol II and/or Pol IV. The low level of UV-induced Arg(+) revertants observed in the AB1157mutD5DumuDC strain indicates that under conditions of disturbed proofreading activity of Pol III and lack of Pol V, UV-induced lesions are bypassed without inducing mutations. The presented results also indicate that Pol V may provide substrates for MFD repair; moreover, we suggest that only those DNA lesions which result from umuDC-directed UV mutagenesis are subject to MFD repair.

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43

Kolodziej, P., and R. A. Young. "RNA polymerase II subunit RPB3 is an essential component of the mRNA transcription apparatus." Molecular and Cellular Biology 9, no. 12 (December 1989): 5387–94. http://dx.doi.org/10.1128/mcb.9.12.5387-5394.1989.

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To improve our understanding of RNA polymerase II, the gene that encodes its third-largest subunit, RPB3, was isolated from a lambda gt11 DNA library by using antibody probes. The RPB3 DNA sequence predicts a 318-amino-acid protein whose sequence was confirmed, in part, by microsequence analysis of the gel-purified RNA polymerase II subunit. RPB3 was found to be an essential single-copy gene that is tightly linked to HIS6 on chromosome IX. An RPB3 temperature-sensitive mutant that arrested growth after three to four generations at the restrictive temperature was isolated. When the mutant was shifted to the restrictive temperature, RNA polymerase II could no longer assemble, previously assembled functional enzyme was depleted, and mRNA levels were consequently reduced. These results demonstrate that RPB3 is an essential component of the mRNA transcription apparatus. Finally, the RPB3 protein is similar in sequence and length to RPC5, a subunit common to RNA polymerases I and III, suggesting that these subunits may play similar roles in RNA polymerases I, II, and III.

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44

Kolodziej, P., and R. A. Young. "RNA polymerase II subunit RPB3 is an essential component of the mRNA transcription apparatus." Molecular and Cellular Biology 9, no. 12 (December 1989): 5387–94. http://dx.doi.org/10.1128/mcb.9.12.5387.

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Abstract:

To improve our understanding of RNA polymerase II, the gene that encodes its third-largest subunit, RPB3, was isolated from a lambda gt11 DNA library by using antibody probes. The RPB3 DNA sequence predicts a 318-amino-acid protein whose sequence was confirmed, in part, by microsequence analysis of the gel-purified RNA polymerase II subunit. RPB3 was found to be an essential single-copy gene that is tightly linked to HIS6 on chromosome IX. An RPB3 temperature-sensitive mutant that arrested growth after three to four generations at the restrictive temperature was isolated. When the mutant was shifted to the restrictive temperature, RNA polymerase II could no longer assemble, previously assembled functional enzyme was depleted, and mRNA levels were consequently reduced. These results demonstrate that RPB3 is an essential component of the mRNA transcription apparatus. Finally, the RPB3 protein is similar in sequence and length to RPC5, a subunit common to RNA polymerases I and III, suggesting that these subunits may play similar roles in RNA polymerases I, II, and III.

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45

GUTIERREZ-HARTMANN, ARTHUR, and JOHN D. BAXTER. "Differential Ability of Various Plasmid DNAs to Sequester Inhibitors of RNA Polymerase III Transcription." DNA 6, no. 3 (June 1987): 231–37. http://dx.doi.org/10.1089/dna.1987.6.231.

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46

Jonczyk, Piotr, Adrianna Nowicka, Iwona J. Fijałkowska, Roel M. Schaaper, and Zygmunt Cieśla. "In Vivo Protein Interactions within theEscherichia coli DNA Polymerase III Core." Journal of Bacteriology 180, no. 6 (March 15, 1998): 1563–66. http://dx.doi.org/10.1128/jb.180.6.1563-1566.1998.

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ABSTRACT The mechanisms that control the fidelity of DNA replication are being investigated by a number of approaches, including detailed kinetic and structural studies. Important tools in these studies are mutant versions of DNA polymerases that affect the fidelity of DNA replication. It has been suggested that proper interactions within the core of DNA polymerase III (Pol III) of Escherichia colicould be essential for maintaining the optimal fidelity of DNA replication (H. Maki and A. Kornberg, Proc. Natl. Acad. Sci. USA 84:4389–4392, 1987). We have been particularly interested in elucidating the physiological role of the interactions between the DnaE (α subunit [possessing DNA polymerase activity]) and DnaQ (ɛ subunit [possessing 3′→5′ exonucleolytic proofreading activity]) proteins. In an attempt to achieve this goal, we have used theSaccharomyces cerevisiae two-hybrid system to analyze specific in vivo protein interactions. In this report, we demonstrate interactions between the DnaE and DnaQ proteins and between the DnaQ and HolE (θ subunit) proteins. We also tested the interactions of the wild-type DnaE and HolE proteins with three well-known mutant forms of DnaQ (MutD5, DnaQ926, and DnaQ49), each of which leads to a strong mutator phenotype. Our results show that the mutD5 anddnaQ926 mutations do not affect the ɛ subunit-α subunit and ɛ subunit-θ subunit interactions. However, thednaQ49 mutation greatly reduces the strength of interaction of the ɛ subunit with both the α and the θ subunits. Thus, the mutator phenotype of dnaQ49 may be the result of an altered conformation of the ɛ protein, which leads to altered interactions within the Pol III core.

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Chaurasiya, K. R., C. Ruslie, M. C. Silva, L. Voortman, P. Nevin, S. Lone, P. J. Beuning, and M. C. Williams. "Polymerase manager protein UmuD directly regulates Escherichia coli DNA polymerase III binding to ssDNA." Nucleic Acids Research 41, no. 19 (July 30, 2013): 8959–68. http://dx.doi.org/10.1093/nar/gkt648.

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48

Sloane, David L., Myron F. Goodman, and Harrison Echols. "The fidelity of base selection by the polymerase subunit of DNA polymerase III holoenzyme." Nucleic Acids Research 16, no. 14 (1988): 6465–75. http://dx.doi.org/10.1093/nar/16.14.6465.

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49

Grúz, Petr, Francesca M. Pisani, Masatomi Shimizu, Masami Yamada, Ikuko Hayashi, Kosuke Morikawa, and Takehiko Nohmi. "Synthetic Activity ofSsoDNA Polymerase Y1, an Archaeal DinB-like DNA Polymerase, Is Stimulated by Processivity Factors Proliferating Cell Nuclear Antigen and Replication Factor C." Journal of Biological Chemistry 276, no. 50 (October 1, 2001): 47394–401. http://dx.doi.org/10.1074/jbc.m107213200.

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DNA replication efficiency is dictated by DNA polymerases (pol) and their associated proteins. The recent discovery of DNA polymerase Y family (DinB/UmuC/RAD30/REV1 superfamily) raises a question of whether the DNA polymerase activities are modified by accessory proteins such as proliferating cell nuclear antigen (PCNA). In fact, the activity of DNA pol IV (DinB) ofEscherichia coliis enhanced upon interaction with the β subunit, the processivity factor of DNA pol III. Here, we report the activity ofSsoDNA pol Y1 encoded by thedbhgene of the archaeonSulfolobus solfataricusis greatly enhanced by the presence of PCNA and replication factor C (RFC).Ssopol Y1per sewas a distributive enzyme but a substantial increase in the processivity was observed on poly(dA)-oligo(dT) in the presence of PCNA (039p or 048p) and RFC. The length of the synthesized DNA product reached at least 200 nucleotides.Ssopol Y1 displayed a higher affinity for DNA compared with pol IV ofE. coli, suggesting that the two DNA polymerases have distinct reason(s) to require the processivity factors for efficient DNA synthesis. The abilities of pol Y1 and pol IV to bypass DNA lesions and their sensitive sites to protease are also discussed.

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50

Xiao, H., R. Crombie, Z. Dong, R. Onrust, and M. O'Donnell. "DNA polymerase III accessory proteins. III. holC and holD encoding chi and psi." Journal of Biological Chemistry 268, no. 16 (June 1993): 11773–78. http://dx.doi.org/10.1016/s0021-9258(19)50266-6.

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Journal articles on the topic 'DNA Polymerase III'

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