Genomes and Genes
dna polymerase i
Summary: A DNA-dependent DNA polymerase characterized in prokaryotes and may be present in higher organisms. It has both 3'-5' and 5'-3' exonuclease activity, but cannot use native double-stranded DNA as template-primer. It is not inhibited by sulfhydryl reagents and is active in both DNA synthesis and repair. EC 126.96.36.199.
- Huang T, Chen C. DNA polymerase I is not required for replication of linear chromosomes in streptomyces. J Bacteriol. 2008;190:755-8 pubmedBoth polA (encoding DNA polymerase I; Pol I) and a paralog were deleted from Streptomyces strains. Despite the UV sensitivity and slow growth caused by the DeltapolA mutation, the double mutant was viable...
- Loh E, Choe J, Loeb L. Highly tolerated amino acid substitutions increase the fidelity of Escherichia coli DNA polymerase I. J Biol Chem. 2007;282:12201-9 pubmed..coli DNA polymerase I and have determined the effects of these substitutions on the fidelity of DNA synthesis...
- Liu X, Hou J, Liu J. Chlamydial DNA polymerase I can bypass lesions in vitro. Biochem Biophys Res Commun. 2006;345:1083-91 pubmedWe found that DNA polymerase I from Chlamydiophila pneumoniae AR39 (CpDNApolI) presents DNA-dependent DNA polymerase activity, but has no detectable 3' exonuclease activity...
- Stuart G, Santos J, Strand M, Van Houten B, Copeland W. Mitochondrial and nuclear DNA defects in Saccharomyces cerevisiae with mutations in DNA polymerase gamma associated with progressive external ophthalmoplegia. Hum Mol Genet. 2006;15:363-74 pubmed..The cellular processes contributing to these observations in the mutant yeast cells are potentially relevant to understanding the pathologies observed in human mitochondrial disease patients. ..
- Pai C, Garcia I, Wang S, Cotterill S, MacNeill S, Kearsey S. GINS inactivation phenotypes reveal two pathways for chromatin association of replicative alpha and epsilon DNA polymerases in fission yeast. Mol Biol Cell. 2009;20:1213-22 pubmed publisher..We suggest that GINS functions in a pathway that involves Cdc45 and is necessary for DNA polymerase epsilon chromatin binding, but that a separate pathway sets up the chromatin association of DNA polymerase alpha. ..
- Wilson N, Abu Shumays R, Gyarfas B, Wang H, Lieberman K, Akeson M, et al. Electronic control of DNA polymerase binding and unbinding to single DNA molecules. ACS Nano. 2009;3:995-1003 pubmed publisher..DNA binding states of the Klenow fragment of Escherichia coli DNA polymerase I (KF) were diagnosed based upon their ionic current signature, and reacted to with submillisecond precision to ..
- Kincaid K, Beckman J, Zivkovic A, Halcomb R, Engels J, Kuchta R. Exploration of factors driving incorporation of unnatural dNTPS into DNA by Klenow fragment (DNA polymerase I) and DNA polymerase alpha. Nucleic Acids Res. 2005;33:2620-8 pubmed..analogues and tested them as substrates for DNA polymerase alpha (pol alpha) and Klenow fragment (exo-) of DNA polymerase I (Escherichia coli)...
- Markovitz A. A new in vivo termination function for DNA polymerase I of Escherichia coli K12. Mol Microbiol. 2005;55:1867-82 pubmed..To explain these results we propose a new in vivo function for wild-type DNA polymerase I in chromosome termination at site(s) not yet identified.
- Kotlyar A, Borovok N, Molotsky T, Fadeev L, Gozin M. In vitro synthesis of uniform poly(dG)-poly(dC) by Klenow exo- fragment of polymerase I. Nucleic Acids Res. 2005;33:525-35 pubmed
- Datta K, Johnson N, LiCata V, von Hippel P. Local conformations and competitive binding affinities of single- and double-stranded primer-template DNA at the polymerization and editing active sites of DNA polymerases. J Biol Chem. 2009;284:17180-93 pubmed publisher..These distributions and the conformational changes in the P/T DNA that occur during template-directed DNA synthesis in solution illuminate some of the mechanisms used by DNA polymerases to assure the fidelity of DNA synthesis. ..
- Errico A, Cosentino C, Rivera T, Losada A, Schwob E, Hunt T, et al. Tipin/Tim1/And1 protein complex promotes Pol alpha chromatin binding and sister chromatid cohesion. EMBO J. 2009;28:3681-92 pubmed publisher..These data indicate that Tipin/Tim1/And1 form a complex that links stabilization of replication fork and establishment of sister chromatid cohesion. ..
- Zhu W, Ukomadu C, Jha S, Senga T, Dhar S, Wohlschlegel J, et al. Mcm10 and And-1/CTF4 recruit DNA polymerase alpha to chromatin for initiation of DNA replication. Genes Dev. 2007;21:2288-99 pubmed..The discovery also adds to the connection between replication initiation and sister chromatid cohesion. ..
- Allen J, Simcha D, Ericson N, Alexander D, Marquette J, Van Biber B, et al. Roles of DNA polymerase I in leading and lagging-strand replication defined by a high-resolution mutation footprint of ColE1 plasmid replication. Nucleic Acids Res. 2011;39:7020-33 pubmed publisherb>DNA polymerase I (pol I) processes RNA primers during lagging-strand synthesis and fills small gaps during DNA repair reactions...
- Berezhna S, Gill J, Lamichhane R, Millar D. Single-molecule Förster resonance energy transfer reveals an innate fidelity checkpoint in DNA polymerase I. J Am Chem Soc. 2012;134:11261-8 pubmed publisher..Using single-molecule Förster resonance energy transfer, we observed individual Escherichia coli DNA polymerase I (Klenow fragment) molecules performing substrate selection...
- Gawel D, Pham P, Fijalkowska I, Jonczyk P, Schaaper R. Role of accessory DNA polymerases in DNA replication in Escherichia coli: analysis of the dnaX36 mutator mutant. J Bacteriol. 2008;190:1730-42 pubmed..Overall, the results provide insight into the interplay of the various DNA polymerases, and of tau subunit, in securing a high fidelity of replication. ..
- Tsutsui Y, Morishita T, Natsume T, Yamashita K, Iwasaki H, Yamao F, et al. Genetic and physical interactions between Schizosaccharomyces pombe Mcl1 and Rad2, Dna2 and DNA polymerase alpha: evidence for a multifunctional role of Mcl1 in DNA replication and repair. Curr Genet. 2005;48:34-43 pubmed..These results strongly suggest that Mcl1p is a functional homologue of Saccharomyces cerevisiae Ctf4p and plays a role in lagging-strand synthesis and Okazaki fragment processing, in addition to DNA repair. ..
- Ricke R, Bielinsky A. A conserved Hsp10-like domain in Mcm10 is required to stabilize the catalytic subunit of DNA polymerase-alpha in budding yeast. J Biol Chem. 2006;281:18414-25 pubmed..The high degree of evolutionary conservation of this domain implies that stabilizing Cdc17 may be a conserved function of Mcm10. ..
- Loh E, Loeb L. Mutability of DNA polymerase I: implications for the creation of mutant DNA polymerases. DNA Repair (Amst). 2005;4:1390-8 pubmed..Analysis of these mutants will help advance our understanding of how DNA polymerases select bases with high fidelity. ..
- Stillman B. DNA polymerases at the replication fork in eukaryotes. Mol Cell. 2008;30:259-60 pubmed publisher..The Kunkel laboratory has recently assigned polymerase (Pol) epsilon as the leading strand polymerase. In a recent issue of Molecular Cell, they now assign Pol delta as the lagging strand polymerase. ..
- Tanaka H, Katou Y, Yagura M, Saitoh K, Itoh T, Araki H, et al. Ctf4 coordinates the progression of helicase and DNA polymerase alpha. Genes Cells. 2009;14:807-20 pubmed publisher..These results lead us to propose that Ctf4 is a key connector between DNA helicase and Pol alpha and is required for the coordinated progression of the replisome. ..
- Trostler M, Delier A, Beckman J, Urban M, Patro J, Spratt T, et al. Discrimination between right and wrong purine dNTPs by DNA polymerase I from Bacillus stearothermophilus. Biochemistry. 2009;48:4633-41 pubmed publisherWe used a series of dATP and dGTP analogues to determine how DNA polymerase I from Bacillus stearothermophilus (BF), a prototypical A family polymerase, uses N-1, N(2), N-3, and N(6) of purine dNTPs to differentiate between right and ..
- Datta K, Wowor A, Richard A, LiCata V. Temperature dependence and thermodynamics of Klenow polymerase binding to primed-template DNA. Biophys J. 2006;90:1739-51 pubmed..In the case of Klenow, surface area burial can account for only about half of the DeltaCp of binding. ..
- Viikov K, Väljamäe P, Sedman J. Yeast mitochondrial DNA polymerase is a highly processive single-subunit enzyme. Mitochondrion. 2011;11:119-26 pubmed publisher..Our observations confirm that in contrast to its homologues in other organisms, Mip1 can function as a single-subunit replicative polymerase. ..
- Wu E, Beese L. The structure of a high fidelity DNA polymerase bound to a mismatched nucleotide reveals an "ajar" intermediate conformation in the nucleotide selection mechanism. J Biol Chem. 2011;286:19758-67 pubmed publisher..Here we report the crystal structure of a high fidelity DNA polymerase I bound to DNA primer-template caught in the act of binding a mismatched (dG:dTTP) nucleoside triphosphate...
- Vaidyanathan V, Cho B. Sequence effects on translesion synthesis of an aminofluorene-DNA adduct: conformational, thermodynamic, and primer extension kinetic studies. Biochemistry. 2012;51:1983-95 pubmed publisher..effect on nucleotide insertion efficiencies catalyzed by the Klenow fragment (exonuclease-deficient) of DNA polymerase I. Our (19)F NMR/ICD/DSC results showed that AF in the CG*A duplex sequence adopts a greater population of S-..
- Hsu C, Chen Y, Tsai S, Tu P, Wang M, Lin J. Interaction of Saccharomyces Cdc13p with Pol1p, Imp4p, Sir4p and Zds2p is involved in telomere replication, telomere maintenance and cell growth control. Nucleic Acids Res. 2004;32:511-21 pubmed..Together, our results provide evidence for the formation of a Cdc13p-mediated telosome complex through its N-terminal region that is involved in telomere maintenance, telomere length regulation and cell growth control. ..
- Santoso Y, Torella J, Kapanidis A. Characterizing single-molecule FRET dynamics with probability distribution analysis. Chemphyschem. 2010;11:2209-19 pubmed publisher..to studying the conformational fluctuations in the unliganded Klenow fragment (KF) of Escherichia coli DNA polymerase I, which allows both confirmation of the consistency of a simple, two-state kinetic model with the observed ..
- McCain M, Meyer A, Schultz S, Glekas A, Spratt T. Fidelity of mispair formation and mispair extension is dependent on the interaction between the minor groove of the primer terminus and Arg668 of DNA polymerase I of Escherichia coli. Biochemistry. 2005;44:5647-59 pubmedThe hydrogen bonding interactions between the Klenow fragment of Escherichia coli DNA polymerase I with the proofreading exonuclease inactivated (KF(-)) and the minor groove of DNA were examined with modified oligodeoxynucleotides in ..
- Golosov A, Warren J, Beese L, Karplus M. The mechanism of the translocation step in DNA replication by DNA polymerase I: a computer simulation analysis. Structure. 2010;18:83-93 pubmed publisher..These roles are consistent with the high level of conservation of Y714 and the two glycine residues at these positions. It is likely that a corresponding mechanism is applicable to other polymerases...
- Camps M, Loeb L. Critical role of R-loops in processing replication blocks. Front Biosci. 2005;10:689-98 pubmed..We propose that downstream of a replication block, RNA at R-loops is extended by DNA polymerase I, opening up the DNA duplex and leading to the recruitment of the replisome...
- Nedelcheva M, Roguev A, Dolapchiev L, Shevchenko A, Taskov H, Shevchenko A, et al. Uncoupling of unwinding from DNA synthesis implies regulation of MCM helicase by Tof1/Mrc1/Csm3 checkpoint complex. J Mol Biol. 2005;347:509-21 pubmed..In concordance with this suggestion, we found that the Tof1/Csm3/Mrc1 checkpoint complex interacts directly with the MCM helicase during both replication fork progression and when the replication fork is stalled. ..
- Markiewicz R, Vrtis K, Rueda D, Romano L. Single-molecule microscopy reveals new insights into nucleotide selection by DNA polymerase I. Nucleic Acids Res. 2012;40:7975-84 pubmed publisher..Our results show that the binding of Escherichia coli DNA polymerase I (Klenow fragment) to a primer-template is stabilized by the presence of the next correct dNTP, even in the ..
- Lone S, Romano L. The role of specific amino acid residues in the active site of Escherichia coli DNA polymerase I on translesion DNA synthesis across from and past an N-2-aminofluorene adduct. Biochemistry. 2007;46:2599-607 pubmed..on replication across from this type of bulky DNA adduct, three active-site mutants of Escherichia coli DNA polymerase I (Klenow fragment) were used to study DNA synthesis on DNA modified with the carcinogen N-2-aminofluorene (AF)...
- Rothwell P, Waksman G. A pre-equilibrium before nucleotide binding limits fingers subdomain closure by Klentaq1. J Biol Chem. 2007;282:28884-92 pubmed..As the only difference between the (E x p/t) complexes is the templating base, it would suggest an important role for the templating base in initial ground state selection. ..
- Joyce C, Potapova O, DeLucia A, Huang X, Basu V, Grindley N. Fingers-closing and other rapid conformational changes in DNA polymerase I (Klenow fragment) and their role in nucleotide selectivity. Biochemistry. 2008;47:6103-16 pubmed publisher..a FRET-based assay for the fingers-closing conformational transition that occurs when a binary complex of DNA polymerase I (Klenow fragment) with a primer-template binds a complementary dNTP and have used this and other fluorescence ..
- Zietlow L, Bessho T. DNA polymerase I-mediated translesion synthesis in RecA-independent DNA interstrand cross-link repair in E. coli. Biochemistry. 2008;47:5460-4 pubmed publisher..We demonstrated that the Klenow fragment (DNA polymerase I) performs translesion synthesis on this model substrate...
- Hile S, Eckert K. Positive correlation between DNA polymerase alpha-primase pausing and mutagenesis within polypyrimidine/polypurine microsatellite sequences. J Mol Biol. 2004;335:745-59 pubmed..Thus, a positive correlation exists between polymerase alpha-primase pausing and mutagenesis within microsatellite DNA alleles. ..
- Singh K, Srivastava A, Patel S, Modak M. Participation of the fingers subdomain of Escherichia coli DNA polymerase I in the strand displacement synthesis of DNA. J Biol Chem. 2007;282:10594-604 pubmed..In prokaryotes, this process is completed by DNA polymerase I by means of strand displacement DNA synthesis and 5 '-nuclease activity...
- Beckman J, Kincaid K, Hocek M, Spratt T, Engels J, Cosstick R, et al. Human DNA polymerase alpha uses a combination of positive and negative selectivity to polymerize purine dNTPs with high fidelity. Biochemistry. 2007;46:448-60 pubmed..Then, to determine whether to add further dNTPs onto the just added nucleotide, pol alpha appears to monitor the shape of the base pair at the primer 3'-terminus. The biological implications of these results are discussed. ..
- Fien K, Cho Y, Lee J, Raychaudhuri S, Tappin I, Hurwitz J. Primer utilization by DNA polymerase alpha-primase is influenced by its interaction with Mcm10p. J Biol Chem. 2004;279:16144-53 pubmed..We suggest that the interaction of Mcm10p with the pol alpha-primase complex, its binding to single-stranded DNA, and its activation of the polymerase complex together contribute to its role in the elongation phase of DNA replication. ..
- Uchiyama M, Wang T. The B-subunit of DNA polymerase alpha-primase associates with the origin recognition complex for initiation of DNA replication. Mol Cell Biol. 2004;24:7419-34 pubmed..Our results thus suggest a role for the recruited Polalpha-primase in the initiation of both leading and lagging strands at the replication origins. ..
- Hastings P, Slack A, Petrosino J, Rosenberg S. Adaptive amplification and point mutation are independent mechanisms: evidence for various stress-inducible mutation mechanisms. PLoS Biol. 2004;2:e399 pubmed..vi) Amplification, and not frameshift mutation, requires DNA polymerase I, demonstrating that mutation is separable from amplification, and also illuminating the amplification ..
- Ono Y, Sakai A, Takechi K, Takio S, Takusagawa M, Takano H. NtPolI-like1 and NtPolI-like2, bacterial DNA polymerase I homologs isolated from BY-2 cultured tobacco cells, encode DNA polymerases engaged in DNA replication in both plastids and mitochondria. Plant Cell Physiol. 2007;48:1679-92 pubmed publisherTwo cDNAs encoding homologs of bacterial DNA polymerase I were isolated from cultured tobacco (Nicotiana tabacum) BY-2 cells, and the corresponding genes were named NtPolI-like1 and NtPolI-like2...
- Garalde D, Simon C, Dahl J, Wang H, Akeson M, Lieberman K. Distinct complexes of DNA polymerase I (Klenow fragment) for base and sugar discrimination during nucleotide substrate selection. J Biol Chem. 2011;286:14480-92 pubmed publisher..The Klenow fragment of Escherichia coli DNA polymerase I (KF) achieves this through a series of conformational transitions that precede the chemical step of ..
- Young M, Theriault S, Li M, Court D. The carboxyl-terminal extension on fungal mitochondrial DNA polymerases: identification of a critical region of the enzyme from Saccharomyces cerevisiae. Yeast. 2006;23:101-16 pubmed..Comparison of this essential segment with the sequences of other fungal mtDNA polymerases revealed novel features shared among the mtDNA polymerases of the Saccharomycetales. ..
- Maiorano D, Cuvier O, Danis E, Mechali M. MCM8 is an MCM2-7-related protein that functions as a DNA helicase during replication elongation and not initiation. Cell. 2005;120:315-28 pubmed..We suggest that MCM8 functions in the elongation step of DNA replication as a helicase that facilitates the recruitment of RPA34 and stimulates the processivity of DNA polymerases at replication foci. ..
- Bermek O, Grindley N, Joyce C. Distinct roles of the active-site Mg2+ ligands, Asp882 and Asp705, of DNA polymerase I (Klenow fragment) during the prechemistry conformational transitions. J Biol Chem. 2011;286:3755-66 pubmed publisher..we developed previously, we have investigated the role of the carboxylate ligands, Asp(705) and Asp(882), of DNA polymerase I (Klenow fragment) in the early prechemistry steps that prepare the active site for catalysis...
- Di Pasquale F, Fischer D, Grohmann D, Restle T, Geyer A, Marx A. Opposed steric constraints in human DNA polymerase beta and E. coli DNA polymerase I. J Am Chem Soc. 2008;130:10748-57 pubmed publisher..coli DNA polymerase I (KF(exo-))...
- Heller R, Kang S, Lam W, Chen S, Chan C, Bell S. Eukaryotic origin-dependent DNA replication in vitro reveals sequential action of DDK and S-CDK kinases. Cell. 2011;146:80-91 pubmed publisher..Our studies identify distinct roles for DDK and S-CDK during helicase activation and support a model in which the leading strand DNA polymerase is recruited prior to origin DNA unwinding and RNA primer synthesis. ..
- Christian T, Romano L, Rueda D. Single-molecule measurements of synthesis by DNA polymerase with base-pair resolution. Proc Natl Acad Sci U S A. 2009;106:21109-14 pubmed publisher..Here we report a single-molecule approach to monitor the movement of E. coli DNA polymerase I (Klenow fragment) on a DNA template during DNA synthesis with single base-pair resolution...
- Tang X, Richards J, Peritz A, Dmochowski I. Photoregulation of DNA polymerase I (Klenow) with caged fluorescent oligodeoxynucleotides. Bioorg Med Chem Lett. 2005;15:5303-6 pubmed..Upon UV photolysis of the DABSYL blocking group under aerobic conditions, fluorescein emission was restored and 50% of the primers were fully extended by KF. ..