1
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Calvo PA, Sastre-Moreno G, Perpiñá C, Guerra S, Martínez-Jiménez MI, Blanco L. The invariant glutamate of human PrimPol DxE motif is critical for its Mn 2+-dependent distinctive activities. DNA Repair (Amst) 2019; 77:65-75. [PMID: 30889508 DOI: 10.1016/j.dnarep.2019.03.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/05/2019] [Accepted: 03/13/2019] [Indexed: 10/27/2022]
Abstract
PrimPol is a human primase/polymerase specialized in downstream repriming of stalled forks during both nuclear and mitochondrial DNA replication. Like most primases and polymerases, PrimPol requires divalent metal cations, as Mg2+ or Mn2+, used as cofactors for catalysis. However, little is known about the consequences of using these two metal cofactors in combination, which would be the most physiological scenario during PrimPol-mediated reactions, and the individual contribution of the putative carboxylate residues (Asp114, Glu116 and Asp280) acting as metal ligands. By site-directed mutagenesis in human PrimPol, we confirmed the catalytic relevance of these three carboxylates, and identified Glu116 as a relevant enhancer of distinctive PrimPol reactions, which are highly dependent on Mn2+. Herein, we evidenced that PrimPol Glu116 contributes to error-prone tolerance of 8oxodG more markedly when both Mg2+ and Mn2+ ions are present. Moreover, Glu116 was important for TLS events mediated by primer/template realignments, and crucial to achieving an optimal primase activity, processes in which Mn2+ is largely preferred. EMSA analysis of PrimPol:ssDNA:dNTP pre-ternary complex indicated a critical role of each metal ligand, and a significant impairment when Glu116 was changed to a more conventional aspartate. These data suggest that PrimPol active site requires a specific motif A (DxE) to favor the use of Mn2+ ions in order to achieve optimal incoming nucleotide stabilization, especially required during primer synthesis.
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Affiliation(s)
- Patricia A Calvo
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM) c/Nicolás Cabrera 1, Cantoblanco, 28049, Madrid, Spain
| | - Guillermo Sastre-Moreno
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM) c/Nicolás Cabrera 1, Cantoblanco, 28049, Madrid, Spain
| | - Cristina Perpiñá
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM) c/Nicolás Cabrera 1, Cantoblanco, 28049, Madrid, Spain
| | - Susana Guerra
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM) c/Nicolás Cabrera 1, Cantoblanco, 28049, Madrid, Spain
| | - María I Martínez-Jiménez
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM) c/Nicolás Cabrera 1, Cantoblanco, 28049, Madrid, Spain
| | - Luis Blanco
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM) c/Nicolás Cabrera 1, Cantoblanco, 28049, Madrid, Spain.
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2
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Lamarche BJ, Orazio NI, Goben B, Meisenhelder J, You Z, Weitzman MD, Hunter T. Repair of protein-linked DNA double strand breaks: Using the adenovirus genome as a model substrate in cell-based assays. DNA Repair (Amst) 2018; 74:80-90. [PMID: 30583959 DOI: 10.1016/j.dnarep.2018.12.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 12/07/2018] [Accepted: 12/07/2018] [Indexed: 11/29/2022]
Abstract
The DNA double strand breaks (DSBs) created during meiotic recombination and during some types of chemotherapy contain protein covalently attached to their 5' termini. Removal of the end-blocking protein is a prerequisite to DSB processing by non-homologous end-joining or homologous recombination. One mechanism for removing the protein involves CtIP-stimulated Mre11-catalyzed nicking of the protein-linked strand distal to the DSB terminus, releasing the end-blocking protein while it remains covalently attached to an oligonucleotide. Much of what is known about this repair process has recently been deciphered through in vitro reconstitution studies. We present here a novel model system based on adenovirus (Ad), which contains the Ad terminal protein covalently linked to the 5' terminus of its dsDNA genome, for studying the repair of 5' protein-linked DSBs in vivo. It was previously shown that the genome of Ad mutants that lack early region 4 (E4) can be joined into concatemers in vivo, suggesting that the Ad terminal protein had been removed from the genome termini prior to ligation. Here we show that during infection with the E4-deleted Ad mutant dl1004, the Ad terminal protein is removed in a manner that recapitulates removal of end-blocking proteins from cellular DSBs. In addition to displaying a dependence on CtIP, and Mre11 acting as the endonuclease, the protein-linked oligonucleotides that are released from the viral genome are similar in size to the oligos that remain attached to Spo11 and Top2 after they are removed from the 5' termini of DSBs during meiotic recombination and etoposide chemotherapy, respectively. The single nucleotide resolution that is possible with this assay, combined with the single sequence context in which the lesion is presented, make it a useful tool for further refining our mechanistic understanding of how blocking proteins are removed from the 5' termini of DSBs.
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Affiliation(s)
- Brandon J Lamarche
- Laboratory of Genetics, Salk Institute for Biological Studies, La Jolla, California, 92037, USA; Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California, 92037, USA
| | - Nicole I Orazio
- Laboratory of Genetics, Salk Institute for Biological Studies, La Jolla, California, 92037, USA
| | - Brittany Goben
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California, 92037, USA
| | - Jill Meisenhelder
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California, 92037, USA
| | - Zhongsheng You
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri, 63110, USA
| | - Matthew D Weitzman
- Laboratory of Genetics, Salk Institute for Biological Studies, La Jolla, California, 92037, USA.
| | - Tony Hunter
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California, 92037, USA.
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3
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Guilliam TA, Doherty AJ. PrimPol-Prime Time to Reprime. Genes (Basel) 2017; 8:genes8010020. [PMID: 28067825 PMCID: PMC5295015 DOI: 10.3390/genes8010020] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 12/09/2016] [Accepted: 12/16/2016] [Indexed: 01/16/2023] Open
Abstract
The complex molecular machines responsible for genome replication encounter many obstacles during their progression along DNA. Tolerance of these obstructions is critical for efficient and timely genome duplication. In recent years, primase-polymerase (PrimPol) has emerged as a new player involved in maintaining eukaryotic replication fork progression. This versatile replicative enzyme, a member of the archaeo-eukaryotic primase (AEP) superfamily, has the capacity to perform a range of template-dependent and independent synthesis activities. Here, we discuss the emerging roles of PrimPol as a leading strand repriming enzyme and describe the mechanisms responsible for recruiting and regulating the enzyme during this process. This review provides an overview and update of the current PrimPol literature, as well as highlighting unanswered questions and potential future avenues of investigation.
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Affiliation(s)
- Thomas A Guilliam
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton BN1 9RQ, UK.
| | - Aidan J Doherty
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton BN1 9RQ, UK.
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4
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Kim J, Song I, Jo A, Shin JH, Cho H, Eoff RL, Guengerich FP, Choi JY. Biochemical analysis of six genetic variants of error-prone human DNA polymerase ι involved in translesion DNA synthesis. Chem Res Toxicol 2014; 27:1837-52. [PMID: 25162224 PMCID: PMC4203391 DOI: 10.1021/tx5002755] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
![]()
DNA
polymerase (pol) ι is the most error-prone among the
Y-family polymerases that participate in translesion synthesis (TLS).
Pol ι can bypass various DNA lesions, e.g., N2-ethyl(Et)G, O6-methyl(Me)G,
8-oxo-7,8-dihydroguanine (8-oxoG), and an abasic site, though frequently
with low fidelity. We assessed the biochemical effects of six reported
genetic variations of human pol ι on its TLS properties, using
the recombinant pol ι (residues 1–445) proteins and DNA
templates containing a G, N2-EtG, O6-MeG, 8-oxoG, or abasic site. The Δ1–25
variant, which is the N-terminal truncation of 25
residues resulting from an initiation codon variant (c.3G > A)
and
also is the formerly misassigned wild-type, exhibited considerably
higher polymerase activity than wild-type with Mg2+ (but
not with Mn2+), coinciding with its steady-state kinetic
data showing a ∼10-fold increase in kcat/Km for nucleotide incorporation
opposite templates (only with Mg2+). The R96G variant,
which lacks a R96 residue known to interact with the incoming nucleotide,
lost much of its polymerase activity, consistent with the kinetic
data displaying 5- to 72-fold decreases in kcat/Km for nucleotide incorporation
opposite templates either with Mg2+ or Mn2+,
except for that opposite N2-EtG with Mn2+ (showing a 9-fold increase for dCTP incorporation). The
Δ1–25 variant bound DNA 20- to 29-fold more tightly than
wild-type (with Mg2+), but the R96G variant bound DNA 2-fold
less tightly than wild-type. The DNA-binding affinity of wild-type,
but not of the Δ1–25 variant, was ∼7-fold stronger
with 0.15 mM Mn2+ than with Mg2+. The results
indicate that the R96G variation severely impairs most of the Mg2+- and Mn2+-dependent TLS abilities of pol ι,
whereas the Δ1–25 variation selectively and substantially
enhances the Mg2+-dependent TLS capability of pol ι,
emphasizing the potential translational importance of these pol ι
genetic variations, e.g., individual differences in TLS, mutation,
and cancer susceptibility to genotoxic carcinogens.
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Affiliation(s)
- Jinsook Kim
- Division of Pharmacology, Department of Molecular Cell Biology, and ‡Department of Physiology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine , Suwon, Gyeonggi-do 440-746, Republic of Korea
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5
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Vaithiyalingam S, Arnett DR, Aggarwal A, Eichman BF, Fanning E, Chazin WJ. Insights into eukaryotic primer synthesis from structures of the p48 subunit of human DNA primase. J Mol Biol 2013; 426:558-69. [PMID: 24239947 DOI: 10.1016/j.jmb.2013.11.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Revised: 11/04/2013] [Accepted: 11/06/2013] [Indexed: 11/25/2022]
Abstract
DNA replication in all organisms requires polymerases to synthesize copies of the genome. DNA polymerases are unable to function on a bare template and require a primer. Primases are crucial RNA polymerases that perform the initial de novo synthesis, generating the first 8-10 nucleotides of the primer. Although structures of archaeal and bacterial primases have provided insights into general priming mechanisms, these proteins are not well conserved with heterodimeric (p48/p58) primases in eukaryotes. Here, we present X-ray crystal structures of the catalytic engine of a eukaryotic primase, which is contained in the p48 subunit. The structures of p48 reveal that eukaryotic primases maintain the conserved catalytic prim fold domain, but with a unique subdomain not found in the archaeal and bacterial primases. Calorimetry experiments reveal that Mn(2+) but not Mg(2+) significantly enhances the binding of nucleotide to primase, which correlates with higher catalytic efficiency in vitro. The structure of p48 with bound UTP and Mn(2+) provides insights into the mechanism of nucleotide synthesis by primase. Substitution of conserved residues involved in either metal or nucleotide binding alter nucleotide binding affinities, and yeast strains containing the corresponding Pri1p substitutions are not viable. Our results reveal that two residues (S160 and H166) in direct contact with the nucleotide were previously unrecognized as critical to the human primase active site. Comparing p48 structures to those of similar polymerases in different states of action suggests changes that would be required to attain a catalytically competent conformation capable of initiating dinucleotide synthesis.
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Affiliation(s)
- Sivaraja Vaithiyalingam
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Diana R Arnett
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA.
| | - Amit Aggarwal
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Brandt F Eichman
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA; Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Ellen Fanning
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
| | - Walter J Chazin
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA; Department of Chemistry, Vanderbilt University, Nashville, TN 37232, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA.
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6
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Korn D. Instantiating a vision: creating the new pathology department at Stanford Medical School. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2011; 7:1-33. [PMID: 21838547 DOI: 10.1146/annurev-pathol-011811-132447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This review represents my best effort to recreate and memorialize events that occurred 44 years ago, when I was invited to join the Stanford University faculty to create, essentially de novo, what rapidly became and remains today one of the very best and most admired departments of pathology in the world. That I was able to accomplish this challenging task I attribute to my holding fast to a somewhat inchoate vision of where the science and practice of pathology would go in future decades, a little bit to my gut instincts and innate ability to spot up-and-coming talent, but a lot to circumstances and good fortune in leading me to a small nucleus of wonderful young professionals of outstanding promise who were willing to join me in "betting the house" that, working together, we could pull off this once-in-a-lifetime opportunity--and we did.
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Affiliation(s)
- David Korn
- Stanford University, Stanford, California 94305, USA
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7
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Frank EG, Woodgate R. Increased catalytic activity and altered fidelity of human DNA polymerase iota in the presence of manganese. J Biol Chem 2007; 282:24689-96. [PMID: 17609217 DOI: 10.1074/jbc.m702159200] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
All DNA polymerases require a divalent cation for catalytic activity. It is generally assumed that Mg(2+) is the physiological cofactor for replicative DNA polymerases in vivo. However, recent studies suggest that certain repair polymerases, such as pol lambda, may preferentially utilize Mn(2+) in vitro. Here we report on the effects of Mn(2+) and Mg(2+) on the enzymatic properties of human DNA polymerase iota (pol iota). pol iota exhibited the greatest activity in the presence of low levels of Mn(2+) (0.05-0.25 mm). Peak activity in the presence of Mg(2+) was observed in the range of 0.1-0.5 mm and was significantly reduced at concentrations >2 mm. Steady-state kinetic analyses revealed that Mn(2+) increases the catalytic activity of pol iota by approximately 30-60,000-fold through a dramatic decrease in the K(m) value for nucleotide incorporation. Interestingly, whereas pol iota preferentially misinserts G opposite T by a factor of approximately 1.4-2.5-fold over the correct base A in the presence of 0.25 and 5 mm Mg(2+), respectively, the correct insertion of A is actually favored 2-fold over the misincorporation of G in the presence of 0.075 mm Mn(2+). Low levels of Mn(2+) also dramatically increased the ability of pol iota to traverse a variety of DNA lesions in vitro. Titration experiments revealed a strong preference of pol iota for Mn(2+) even when Mg(2+) is present in a >10-fold excess. Our observations therefore raise the intriguing possibility that the cation utilized by pol iota in vivo may actually be Mn(2+) rather than Mg(2+), as tacitly assumed.
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Affiliation(s)
- Ekaterina G Frank
- Laboratory of Genomic Integrity, NICHD, National Institutes of Health, Bethesda, Maryland 20892-2725, USA
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8
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Boxer LM, Korn D. Structural and enzymological characterization of the homogeneous deoxyribonucleic acid polymerase from Mycoplasma orale. Biochemistry 2002. [DOI: 10.1021/bi00588a039] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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9
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Venegas J, Solari A. Purification and characterization of a beta-like DNA polymerase from Trypanosoma cruzi. Mol Biochem Parasitol 1995; 73:53-62. [PMID: 8577347 DOI: 10.1016/0166-6851(94)00091-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
A DNA polymerase was purified to near homogeneity from Trypanosoma cruzi epimastigotes. This preparation had a major polypeptide of 50 kDa and a minor band of 45 kDa. SDS-PAGE studies and a novel colorimetric activity gel technique demonstrated that the 50-kDa polypeptide chain is the catalytic subunit of this T. cruzi DNA polymerase. Western blot analysis of different purification stage fractions strongly suggests that this 50-kDa protein is the intact catalytic subunit and does not correspond to a degradation product from a larger one. This T. cruzi DNA polymerase is insensitive to aphidicolin, butylphenyldeoxyguanosine triphosphate, berenil, ethidium bromide and N-ethylmaleimide, but is markedly inhibited by the dideoxythymidine triphosphate analogue. Studies with different DNA templates showed that the DNA polymerase prefers activated DNA as substrate and that it cannot elongate oligoriboadenylate primers. The data presented in this paper are consistent with the hypothesis that this enzyme corresponds to a beta-like DNA polymerase present in the parasitic protozoon T. cruzi.
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Affiliation(s)
- J Venegas
- Departamento de Bioquímica, Facultad de Medicina, Universidad de Chile, Santiago, Chile
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10
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Budd ME, Campbell JL. Purification and enzymatic and functional characterization of DNA polymerase beta-like enzyme, POL4. expressed during yeast meiosis. Methods Enzymol 1995; 262:108-30. [PMID: 8594342 DOI: 10.1016/0076-6879(95)62014-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- M E Budd
- Department of Chemistry, California Institute of Technology, Pasadena 91125, USA
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11
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Chen MS, Suttmann RT, Papp E, Cannon PD, McRoberts MJ, Bach C, Copeland WC, Wang TS. Selective action of 4'-azidothymidine triphosphate on reverse transcriptase of human immunodeficiency virus type 1 and human DNA polymerases alpha and beta. Biochemistry 1993; 32:6002-10. [PMID: 7685186 DOI: 10.1021/bi00074a011] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
4'-Azidothymidine (ADRT) is a novel nucleoside analogue that exhibits potent inhibitory activity against the replication of human immunodeficiency virus (HIV) in lymphocytes. The mechanisms by which ADRT inhibits HIV reverse transcriptase (HIV-RT) as ADRT 5'-triphosphate (ADRT-TP), the active intracellular metabolite of ADRT, and as the ADRT-MP molecule incorporated into DNA were examined and compared to their effects on human DNA polymerases alpha and beta. Inhibition of HIV-RT by ADRT-TP is competitive against TTP and is more potent against RNA to DNA synthesis (Ki = 0.009 microM versus Km = 3.3 microM for TTP) than it is against DNA to DNA synthesis (Ki = 0.95 microM versus Km = 16.3 microM for TTP). ADRT-TP is also a more potent inhibitor for primer elongation on RNA template than on DNA template. ADRT-TP is a poor inhibitor of human DNA polymerases alpha (Ki = 62.5 microM) and beta (Ki = 150 microM) (Chen et al., 1992). The consequences of ADRT incorporation into DNA are strikingly different for the HIV-RT and for human DNA polymerases alpha and beta. DNA polymerases alpha and beta incorporate a single ADRT-MP molecule into nascent DNA at a very slow rate and continue to elongate. They are unable to incorporate a second consecutive ADRT-MP. However, HIV-RT is able to efficiently incorporate two consecutive ADRT molecules. Incorporation of two consecutive ADRT-MP molecules by HIV-RT prevents further DNA chain elongation. Incorporation of two ADRT-MP molecules separated by one deoxyribonucleoside monophosphate (dAMP, dCMP, or dGMP) also abolishes DNA chain elongation by HIV-RT.
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Affiliation(s)
- M S Chen
- Institute of Biochemistry and Cell Biology, Syntex Research, Palo Alto, California 94304
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12
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Abstract
Inhibitory and substrate properties of analogs of deoxyribonucleoside triphosphates toward DNA polymerases are reviewed. A general introduction is followed by a description of DNA polymerases and the reaction that they catalyze, and sites at which substrate analogs may inhibit them. Effects of modifications in the major family of compounds, nucleotide derivatives, at the base, sugar and triphosphate portions of the molecule, are summarized with respect to retention of substrate properties and generation of inhibitory properties. Structure-activity relationships and the basis of selectivity in the second family of compounds, deoxyribonucleotide mimics, are also presented. Conclusions are drawn regarding the structural basis of inhibitor selectivity and mechanism, relationship between in vitro and in vivo effects of inhibitors, and the promise of inhibitors as probes for study of active sites of DNA polymerases.
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Affiliation(s)
- G E Wright
- Department of Pharmacology, University of Massachusetts Medical School, Worcester 01655
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13
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Induction of beta-polymerase mRNA by DNA-damaging agents in Chinese hamster ovary cells. Mol Cell Biol 1989. [PMID: 2710127 DOI: 10.1128/mcb.9.2.851] [Citation(s) in RCA: 108] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Only a few of the genes involved in DNA repair in mammalian cells have been isolated, and induction of a DNA repair gene in response to DNA damage has not yet been established. DNA polymerase beta (beta-polymerase) appears to have a synthetic role in DNA repair after certain types of DNA damage. Here we show that the level of beta-polymerase mRNA is increased in CHO cells after treatment with several DNA-damaging agents.
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14
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DiGiuseppe JA, Wright GE, Dresler SL. A kinetic study of rat recombinant DNA polymerase beta: detection of a slow (hysteretic) transition in polymerase activity and inhibition by butylphenyl-deoxyguanosine triphosphate. Nucleic Acids Res 1989; 17:3079-89. [PMID: 2726452 PMCID: PMC317715 DOI: 10.1093/nar/17.8.3079] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
We have identified and characterized a distinct non-linearity in the time course of the reaction of mammalian DNA polymerase beta with synthetic polynucleotides. Nucleotide incorporation is biphasic; an initial burst of activity decays exponentially to a lower steady-state velocity. This slow transition in polymerase activity is not due to substrate depletion, abortive complex formation, or enzyme inactivation. The data are consistent with description of the beta-polymerase as a hysteretic enzyme, a finding which provides a potential explanation for the non-hyperbolic kinetics which have been reported previously for this polymerase. We have also found, in contrast to some previous data, that the nucleotide analogue, N2-(p-n-butylphenyl)-2'-deoxyguanosine-5'-triphosphate (BuPdGTP), is an inhibitor of the beta-polymerase. When poly(dC).oligo(dG) is used as template.primer, inhibition of the initial velocity is competitive with dGTP with a Ki of 1.25 microM. On activated DNA, however, beta-polymerase displays sensitivity to BuPdGTP which overlaps with that previously reported for DNA polymerase delta; 100 microM BuPdGTP is required to inhibit the initial velocity of a dGTP-deficient, truncated assay. Finally, we demonstrate that, in addition to its inhibition of initial velocity, BuPdGTP also modulates both the rate constant of the slow transition in polymerase activity, and the steady-state velocity of the beta-polymerase.
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Affiliation(s)
- J A DiGiuseppe
- Department of Pathology, Washington University School of Medicine, St Louis, MO 63110
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15
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Fornace AJ, Zmudzka B, Hollander MC, Wilson SH. Induction of beta-polymerase mRNA by DNA-damaging agents in Chinese hamster ovary cells. Mol Cell Biol 1989; 9:851-3. [PMID: 2710127 PMCID: PMC362667 DOI: 10.1128/mcb.9.2.851-853.1989] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Only a few of the genes involved in DNA repair in mammalian cells have been isolated, and induction of a DNA repair gene in response to DNA damage has not yet been established. DNA polymerase beta (beta-polymerase) appears to have a synthetic role in DNA repair after certain types of DNA damage. Here we show that the level of beta-polymerase mRNA is increased in CHO cells after treatment with several DNA-damaging agents.
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Affiliation(s)
- A J Fornace
- Radiation Oncology Branch, National Cancer Institute, Bethesda, Maryland 20892
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16
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Zmudzka BZ, Fornace A, Collins J, Wilson SH. Characterization of DNA polymerase beta mRNA: cell-cycle and growth response in cultured human cells. Nucleic Acids Res 1988; 16:9587-96. [PMID: 2460824 PMCID: PMC338765 DOI: 10.1093/nar/16.20.9587] [Citation(s) in RCA: 73] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
DNA polymerase beta (beta-polymerase) is a housekeeping enzyme involved in DNA repair in vertebrate cells. We used a cDNA probe to study abundance of beta-polymerase mRNA in cultured human cells. The mRNA level in synchronized HeLa cells, representing different stages of the cell-cycle, varied only slightly. Contact inhibited fibroblasts AG-1522 contained the same level of mRNA as growing cells. The steady-state level of mRNA in fibroblasts is equivalent to 6 molecules per cell. The results indicate that the beta-polymerase transcript is "low abundance" and is neither cell-cycle nor growth phase responsive.
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Affiliation(s)
- B Z Zmudzka
- Laboratory of Biochemistry, National Cancer Institute, Bethesda, MD 20892
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17
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Madsen P, Celis JE. S-phase patterns of cyclin (PCNA) antigen staining resemble topographical patterns of DNA synthesis. A role for cyclin in DNA replication? FEBS Lett 1985; 193:5-11. [PMID: 2415394 DOI: 10.1016/0014-5793(85)80068-5] [Citation(s) in RCA: 89] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The sequence of cyclin (proliferating cell nuclear antigen, PCNA), antigen staining throughout the cell cycle of African green monkey kidney cells (BS-C-1) has been determined by indirect immunofluorescence using PCNA autoantibodies specific for this protein. Patterns of cyclin staining observed between the beginning of S-phase and maximum DNA synthesis are similar to those reported in human AMA cells [(1985) Proc. Natl. Acad. Sci. USA 82, 3262-3266], while those detected thereafter are significantly different; the most striking feature being the continuous staining of the nucleoli up to or very near the S/G2 border of the cell cycle. Using [3H]thymidine autoradiography and indirect immunofluorescence of the same cells we show a remarkable correlation between cyclin antigen distribution and topographical patterns of DNA synthesis. In addition, we present evidence showing that DNase I treatment of Triton-extracted monolayers abolishes cyclin antigen staining but does not result in a substantial release of this protein. Taken together the above observations argue for a role of cyclin in some aspect of DNA replication.
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18
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Kunkel TA. The mutational specificity of DNA polymerase-beta during in vitro DNA synthesis. Production of frameshift, base substitution, and deletion mutations. J Biol Chem 1985. [DOI: 10.1016/s0021-9258(18)89090-1] [Citation(s) in RCA: 231] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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19
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Abstract
The mechanism by which DNA polymerase discriminates between complementary and noncomplementary nucleotides for insertion into a primer terminus has been investigated. Apparent kinetic constants for the insertion of dGTP and dATP into the hook polymer d(C)194-d(G)12 with Escherichia coli DNA polymerase I (large fragment) were determined. The results suggest that the high specificity of base selection by DNA polymerase I is achieved by utilization of both Km and Vmax differences between complementary and noncomplementary nucleotides. The molecular basis for the increased error frequency observed with DNA polymerase I in the presence of Mn2+ has also been investigated. Our studies demonstrate that when Mn2+ is substituted for Mg2+, there is a higher ratio of insertion of incorrect to correct dNTP by the polymerase activity, accompanied by a decreased hydrolysis of a mismatched dNMP relative to a matched dNMP at the primer terminus by the 3',5' exonuclease activity. Kinetic analysis revealed that in the presence of Mn2+, the kcat for insertion of a complementary dNTP is reduced, whereas the catalytic rate for the insertion of a mismatched nucleotide is increased. The apparent Km values for either complementary or noncomplementary nucleotide substrates are not significantly altered when Mg2+ is replaced by Mn2+. The rate of hydrolysis of a mismatched dNMP at the primer terminus is greater in the presence of Mg2+ vs. Mn2+, whereas the rate of hydrolysis of a properly base-paired terminal nucleotide is greater in Mn2+ vs. Mg2+. These studies demonstrate that both the accuracy of base selection by the polymerase activity and the specificity of hydrolysis by the 3',5' exonuclease activity are altered by the substitution of Mn2+ for Mg2+.
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20
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Biswas SB, Kornberg A. Nucleoside triphosphate binding to DNA polymerase III holoenzyme of Escherichia coli. A direct photoaffinity labeling study. J Biol Chem 1984. [DOI: 10.1016/s0021-9258(17)42890-0] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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21
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22
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Philippe M, Wang TS, Hanawalt PC, Korn D. DNA synthesis on UV irradiated model templates using human DNA polymerases alpha and beta: primer slippage to account for evident transdimer continuity in product. Biochimie 1982; 64:783-8. [PMID: 6814528 DOI: 10.1016/s0300-9084(82)80129-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
We have studied the comparative behavior of human DNA polymerases alpha and beta on a polynucleotide template of dT100 with dA15 covalently attached at the 3' end to serve as primer when defined numbers of pyrimidine dimers are introduced by UV (254 nm) irradiation. We have obtained the surprising result that with both alpha and beta polymerases the incorporation of labelled dATP is enhanced when the template has been irradiated (maximum value at 1000 J/m2 UV incident dose). In the presence of Mn2+, DNA polymerase beta produces a product size corresponding to full copying of the template whether irradiated or not. In marked contrast DNA polymerase alpha produces only short products on unirradiated strands but full copying of irradiated templates. Evidently both polymerases utilize a much larger fraction of the template pool following UV irradiation.
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23
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Tanaka S, Hu SZ, Wang TS, Korn D. Preparation and preliminary characterization of monoclonal antibodies against human DNA polymerase alpha. J Biol Chem 1982. [DOI: 10.1016/s0021-9258(18)34343-6] [Citation(s) in RCA: 184] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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24
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Filpula D, Fisher P, Korn D. DNA polymerase-alpha. Common polypeptide core structure of three enzyme forms from human KB cells. J Biol Chem 1982. [DOI: 10.1016/s0021-9258(19)68143-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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25
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Enzymological characterization of KB cell DNA polymerase-alpha. Regulation of template binding by nucleic acid base composition. J Biol Chem 1981. [DOI: 10.1016/s0021-9258(19)70108-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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26
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Mosbaugh D, Meyer R. Interaction of mammalian deoxyribonuclease V, a double strand 3' to 5' and 5' to 3' exonuclease, with deoxyribonucleic acid polymerase-beta from the Novikoff hepatoma. J Biol Chem 1980. [DOI: 10.1016/s0021-9258(19)70455-4] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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27
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Planck SR, Tanabe K, Wilson SH. Distinction between mouse DNA polymerases alpha and beta by tryptic peptide mapping. Nucleic Acids Res 1980; 8:2771-82. [PMID: 7433094 PMCID: PMC324119 DOI: 10.1093/nar/8.12.2771] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Results presented here and in a previous paper (Tanabe et al. (1979) Biochemistry 18, 3401--3406) indicate that mouse beta-polymerase is a single polypeptide with an apparent molecular weight of 40,000. This polypeptide has now been analyzed by tryptic peptide mapping. Comparison of the results with identical analysis of mouse alpha-polymerase reveals that the tryptic peptides derived from the two enzymes are different. These results indicate that beta-polymerase is neither a subunit of alpha-polymerase nor a proteolytic degradation product of alpha-polymerase.
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28
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Wang TS, Korn D. Reactivity of KB cell deoxyribonucleic acid polymerases alpha and beta with nicked and gapped deoxyribonucleic acid. Biochemistry 1980; 19:1782-90. [PMID: 6246934 DOI: 10.1021/bi00550a009] [Citation(s) in RCA: 85] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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29
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Gregerson DS, Reid TW. Properties of the reverse transcription of synthetic and hamster retroviral RNA by avian and hamster viral polymerases. Biochem Biophys Res Commun 1980; 93:720-8. [PMID: 6155913 DOI: 10.1016/0006-291x(80)91137-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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30
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Fisher P, Korn D. Enzymological characterization of KB cell DNA polymerase-alpha. II. Specificity of the protein-nucleic acid interaction. J Biol Chem 1979. [DOI: 10.1016/s0021-9258(19)86626-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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31
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Popenoe EA, Schmaeler MA. Interaction of human DNA polymerase beta with ions of copper, lead, and cadmium. Arch Biochem Biophys 1979; 196:109-20. [PMID: 507799 DOI: 10.1016/0003-9861(79)90557-5] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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32
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Challberg M, Englund P. The effect of template secondary structure on vaccinia DNA polymerase. J Biol Chem 1979. [DOI: 10.1016/s0021-9258(18)36020-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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33
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Fisher PA, Wang TS, Korn D. Enzymological characterization of DNA polymerase alpha. Basic catalytic properties processivity, and gap utilization of the homogeneous enzyme from human KB cells. J Biol Chem 1979. [DOI: 10.1016/s0021-9258(18)50528-7] [Citation(s) in RCA: 85] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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34
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Waser J, Hübscher U, Kuenzle CC, Spadari S. DNA polymerase beta from brain neurons is a repair enzyme. EUROPEAN JOURNAL OF BIOCHEMISTRY 1979; 97:361-8. [PMID: 467424 DOI: 10.1111/j.1432-1033.1979.tb13122.x] [Citation(s) in RCA: 91] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
DNA polymerase beta was isolated from rat cortex neurons and characterised. Its properties were strikingly similar to those of other mammalian beta-polymerases. In adult rats, this was the major DNA polymerase occurring in neuronal nuclei, which contained no alpha-polymerase, 99.2% beta-polymerase and only 0.8% gamma-polymerase. Isolated neuronal nuclei of this developmental stage were shown to perform ultraviolet-induced repair DNA synthesis in vitro. Since beta-polymerase was virtually the exclusive DNA polymerase in these nuclei it was concluded that the beta enzyme was responsible for the observed DNA repair. This was further substantiated by demonstrating a virtually complete suppression of DNA repair in irradiated nuclei by 2',3'-dideoxyribosylthymine 5'-triphosphate (d2TTP), a potent beta-polymerase inhibitor. However, the presence of minute amounts of gamma-polymerase in neuronal nuclei and its susceptibility to d2TTP did not allow one to rule out an ancillary role of DNA polymerase gamma in DNA repair. In view of the similarity of the neuronal DNA polymerase beta with all other mammalian beta-polymerases it may be speculated that the ability to perform repair DNA synthesis is not unique to the neuronal enzyme but is a general function of all beta-polymerases.
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35
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36
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Mildvan AS, Loeb LA. The role of metal ions in the mechanisms of DNA and RNA polymerases. CRC CRITICAL REVIEWS IN BIOCHEMISTRY 1979; 6:219-44. [PMID: 378534 DOI: 10.3109/10409237909102564] [Citation(s) in RCA: 86] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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