501
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Hamdan S, Carr PD, Brown SE, Ollis DL, Dixon NE. Structural basis for proofreading during replication of the Escherichia coli chromosome. Structure 2002; 10:535-46. [PMID: 11937058 DOI: 10.1016/s0969-2126(02)00738-4] [Citation(s) in RCA: 118] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The epsilon subunit of the Escherichia coli replicative DNA polymerase III is the proofreading 3'-5' exonuclease. Structures of its catalytic N-terminal domain (epsilon186) were determined at two pH values (5.8 and 8.5) at resolutions of 1.7-1.8 A, in complex with two Mn(II) ions and a nucleotide product of its reaction, thymidine 5'-monophosphate. The protein structure is built around a core five-stranded beta sheet that is a common feature of members of the DnaQ superfamily. The structures were identical, except for differences in the way TMP and water molecules are coordinated to the binuclear metal center in the active site. These data are used to develop a mechanism for epsilon and to produce a plausible model of the complex of epsilon186 with DNA.
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Affiliation(s)
- Samir Hamdan
- Research School of Chemistry, Australian National University, Canberra, ACT, Australia
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502
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Wagner J, Etienne H, Janel-Bintz R, Fuchs RPP. Genetics of mutagenesis in E. coli: various combinations of translesion polymerases (Pol II, IV and V) deal with lesion/sequence context diversity. DNA Repair (Amst) 2002; 1:159-67. [PMID: 12509262 DOI: 10.1016/s1568-7864(01)00012-x] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The biochemistry and genetics of translesion synthesis (TLS) and, as a consequence, of mutagenesis has recently received much attention in view of the discovery of novel DNA polymerases, most of which belong to the Y family. These distributive and low fidelity enzymes assist the progression of the high fidelity replication complex in the bypass of DNA lesions that normally hinder its progression. The present paper extends our previous observation that in Escherichia coli all three SOS-inducible DNA polymerases (Pol II, IV and V) are involved in TLS and mutagenesis. The genetic control of frameshift mutation pathways induced by N-2-acetylaminofluorene (AAF) adducts or by oxidative lesions induced by methylene blue and visible light is investigated. The data show various examples of mutation pathways with an absolute requirement for a specific combination of DNA polymerases and, in contrast, other examples where two DNA polymerases exhibit functional redundancy within the same pathway. We suggest that cells respond to the challenge of replicating DNA templates potentially containing a large diversity of DNA lesions by using a pool of accessory DNA polymerases with relaxed specificities that assist the high fidelity replicase.
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Affiliation(s)
- Jérôme Wagner
- UPR conventionnée de l'Université Louis Pasteur de Strasbourg, UPR 9003 du CNRS, Cancérogenèse et Mutagenèse Moléculaire et Structurale, IRCAD, Hôpitaux Universitaires BP 424, 67091, Strasbourg, France
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503
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Washington MT, Johnson RE, Prakash L, Prakash S. Human DINB1-encoded DNA polymerase kappa is a promiscuous extender of mispaired primer termini. Proc Natl Acad Sci U S A 2002; 99:1910-4. [PMID: 11842189 PMCID: PMC122293 DOI: 10.1073/pnas.032594399] [Citation(s) in RCA: 127] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2001] [Indexed: 11/18/2022] Open
Abstract
Both in yeast and humans, DNA polymerase (Pol) (eta) functions in the error-free replication of UV-damaged DNA, and Pol(eta) has the unique ability to efficiently replicate through a cis-syn thymine-thymine (T-T) dimer by inserting two As opposite the two Ts of the dimer. Although human DINB1-encoded Pol(kappa) belongs to the same protein family as Pol(eta), Pol(kappa) shows no ability to bypass this DNA lesion and its biological function has remained unclear. Here, we examine Pol(kappa) for its ability to extend from primer-terminal mispairs opposite nondamaged and damaged DNA templates. We find that Pol(kappa) is a promiscuous extender of primer-terminal mispairs opposite nondamaged DNA templates, and interestingly, it is also very efficient at extending from a G opposite the 3'T of a T-T dimer. These observations provide biochemical evidence for a role of Pol(kappa) in the extension of mismatched base pairs during normal DNA replication, and in addition, they implicate Pol(kappa) in the mutagenic bypass of T-T dimers. In its proficient mismatch extension ability, Pol(kappa) is more similar to the unrelated DNA polymerase zeta than it is to the phylogenetically related Pol(eta) or Pol(iota). Thus, in humans, Pol(kappa) would compete with Pol(zeta) for the extension of mismatched base pairs on damaged and undamaged DNAs.
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Affiliation(s)
- M Todd Washington
- Sealy Center for Molecular Science, University of Texas Medical Branch at Galveston, 6.104 Blocker Medical Research Building, 11th and Mechanic Streets, Galveston, TX 77555-1061, USA
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504
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Summerer D, Marx A. Differential minor groove interactions between DNA polymerase and sugar backbone of primer and template strands. J Am Chem Soc 2002; 124:910-1. [PMID: 11829591 DOI: 10.1021/ja017244j] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
DNA polymerases are the key enzymes for DNA synthesis involved in DNA replication, recombination, and repair. These enzymes undergo manifold contacts with the primer-template-substrates reaching up to several nucleotide pairs beyond the catalytic centre. To evaluate these enzyme contacts with the DNA substrates we applied novel synthetic steric probes in functional studies. We found that through application of the these probes valuable insights into DNA polymerase function can be gained, which might be useful for the design of new DNA polymerase-based nucleotide variation detection strategies.
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Affiliation(s)
- Daniel Summerer
- Kekulé-Institut für Organische Chemie und Biochemie Universität Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany
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505
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Goel A, Ellenberger T, Frank-Kamenetskii MD, Herschbach D. Unifying themes in DNA replication: reconciling single molecule kinetic studies with structural data on DNA polymerases. J Biomol Struct Dyn 2002; 19:571-84. [PMID: 11843619 DOI: 10.1080/07391102.2002.10506764] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Structural data suggest that DNA polymerases, from at least three different families, employ common strategies for carrying out DNA replication. Universal features include a large conformational change in the enzyme-template complex and a conserved active-site geometry that imposes a sharp kink at the 5 end of the template strand. Recent single molecule experiments have shown that stretching the DNA template markedly alters the rate of DNA synthesis catalyzed by these motor enzymes. From these data, it was previously inferred that T7 DNA polymerase and two related enzymes convert two or four (depending on the enzyme) single-stranded (ss) template bases to double helix geometry in the polymerase active site during each catalytic cycle. We discuss structural data on related DNA polymerases, which suggest that only one (ss) template base is contracted to dsDNA geometry during the rate-limiting step of each replication cycle. Previous interpretations relied upon the global stretching curves for DNA polymers alone (with no reference to the enzyme or the structure of the transition state). In contrast, we present a structurally guided model that presumes the force dependence of the replication rate is governed chiefly by local interactions in the immediate vicinity of the enzyme s active site. Our analysis reconciles single molecule kinetic studies with structural data on DNA polymerases.
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Affiliation(s)
- Anita Goel
- Department of Physics and Harvard-MIT Joint Division of Health Sciences and Technology, Harvard University, Cambridge, MA 02138, USA.
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506
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Broughton BC, Cordonnier A, Kleijer WJ, Jaspers NGJ, Fawcett H, Raams A, Garritsen VH, Stary A, Avril MF, Boudsocq F, Masutani C, Hanaoka F, Fuchs RP, Sarasin A, Lehmann AR. Molecular analysis of mutations in DNA polymerase eta in xeroderma pigmentosum-variant patients. Proc Natl Acad Sci U S A 2002; 99:815-20. [PMID: 11773631 PMCID: PMC117388 DOI: 10.1073/pnas.022473899] [Citation(s) in RCA: 115] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Xeroderma pigmentosum variant (XP-V) cells are deficient in their ability to synthesize intact daughter DNA strands after UV irradiation. This deficiency results from mutations in the gene encoding DNA polymerase eta, which is required for effecting translesion synthesis (TLS) past UV photoproducts. We have developed a simple cellular procedure to identify XP-V cell strains, and have subsequently analyzed the mutations in 21 patients with XP-V. The 16 mutations that we have identified fall into three categories. Many of them result in severe truncations of the protein and are effectively null alleles. However, we have also identified five missense mutations located in the conserved catalytic domain of the protein. Extracts of cells falling into these two categories are defective in the ability to carry out TLS past sites of DNA damage. Three mutations cause truncations at the C terminus such that the catalytic domains are intact, and extracts from these cells are able to carry out TLS. From our previous work, however, we anticipate that protein in these cells will not be localized in the nucleus nor will it be relocalized into replication foci during DNA replication. The spectrum of both missense and truncating mutations is markedly skewed toward the N-terminal half of the protein. Two of the missense mutations are predicted to affect the interaction with DNA, the others are likely to disrupt the three-dimensional structure of the protein. There is a wide variability in clinical features among patients, which is not obviously related to the site or type of mutation.
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Affiliation(s)
- Bernard C Broughton
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton BN1 9RR, United Kingdom
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507
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Washington MT, Prakash L, Prakash S. Yeast DNA polymerase eta utilizes an induced-fit mechanism of nucleotide incorporation. Cell 2001; 107:917-27. [PMID: 11779467 DOI: 10.1016/s0092-8674(01)00613-4] [Citation(s) in RCA: 105] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
DNA polymerase eta (Poleta) is unique among eukaryotic DNA polymerases in its proficient ability to replicate through distorting DNA lesions, and Poleta synthesizes DNA with a low fidelity. Here, we use pre-steady-state kinetics to investigate the mechanism of nucleotide incorporation by Poleta and show that it utilizes an induced-fit mechanism to selectively incorporate the correct nucleotide. Poleta discriminates poorly between the correct and incorrect nucleotide at both the initial nucleotide binding step and at the subsequent induced-fit conformational change step, which precedes the chemical step of phosphodiester bond formation. This property enables Poleta to bypass lesions with distorted DNA geometries, and it bestows upon the enzyme a low fidelity.
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Affiliation(s)
- M T Washington
- Sealy Center for Molecular Science, University of Texas Medical Branch at Galveston, 6.104 Blocker Medical Research Building, 11th and Mechanic Streets, Galveston, TX 77555, USA
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508
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Glick E, Vigna KL, Loeb LA. Mutations in human DNA polymerase eta motif II alter bypass of DNA lesions. EMBO J 2001; 20:7303-12. [PMID: 11743006 PMCID: PMC125802 DOI: 10.1093/emboj/20.24.7303] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2001] [Revised: 10/31/2001] [Accepted: 11/02/2001] [Indexed: 11/14/2022] Open
Abstract
Human DNA polymerase eta (hPol eta) is one of the newly identified Y-family of DNA polymerases. These polymerases synthesize past template lesions that are postulated to block replication fork progression. hPol eta accurately bypasses UV-associated cis-syn cyclobutane thymine dimers in vitro and contributes to normal resistance to sunlight-induced skin cancer. We describe here mutational analysis of motif II, a highly conserved sequence, recently reported to reside in the fingers domain and to form part of the active site in Y-family DNA polymerases. We used a yeast-based complementation system to isolate biologically active mutants created by random sequence mutagenesis, synthesized the mutant proteins in vitro and assessed their ability to bypass thymine dimers. The mutability of motif II in 210 active mutants has parallels with natural evolution and identifies Tyr52 and Ala54 as prime candidates for involvement in catalytic activity or bypass. We describe the ability of hPol eta S62G, a mutant polymerase with enhanced activity, to bypass five other site-specific lesions. Our results may serve as a prototype for studying other members of the Y-family DNA polymerases.
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Affiliation(s)
| | | | - Lawrence A. Loeb
- The Joseph Gottstein Memorial Cancer Research Laboratory, Department of Pathology, Box 357705, University of Washington, Seattle, WA 98195-357705, USA
Corresponding author e-mail:
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509
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Gearhart PJ, Wood RD. Emerging links between hypermutation of antibody genes and DNA polymerases. Nat Rev Immunol 2001; 1:187-92. [PMID: 11905827 DOI: 10.1038/35105009] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Substantial antibody variability is created when nucleotide substitutions are introduced into immunoglobulin variable genes by a controlled process of hypermutation. Evidence points to a mechanism involving DNA repair events at sites of targeted breaks. In vertebrate cells, there are many recently identified DNA polymerases that inaccurately copy templates. Some of these are candidates for enzymes that introduce base changes during hypermutation. Recent research has focused on possible roles for DNA polymerases zeta (POLZ), eta (POLH), iota (POLI), and mu (POLM) in the process.
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Affiliation(s)
- P J Gearhart
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, Maryland 21224, USA.
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510
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Boudsocq F, Iwai S, Hanaoka F, Woodgate R. Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4): an archaeal DinB-like DNA polymerase with lesion-bypass properties akin to eukaryotic poleta. Nucleic Acids Res 2001; 29:4607-16. [PMID: 11713310 PMCID: PMC92520 DOI: 10.1093/nar/29.22.4607] [Citation(s) in RCA: 188] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Phylogenetic analysis of Y-family DNA polymerases suggests that it can be subdivided into several discrete branches consisting of UmuC/DinB/Rev1/Rad30/Rad30A and Rad30B. The most diverse is the DinB family that is found in all three kingdoms of life. Searches of the complete genome of the crenarchaeon Sulfolobus solfataricus P2 reveal that it possesses a DinB homolog that has been termed DNA polymerase IV (Dpo4). We have overproduced and purified native Dpo4 protein and report here its enzymatic characterization. Dpo4 is thermostable, but can also synthesize DNA at 37 degrees C. Under these conditions, the enzyme exhibits misinsertion fidelities in the range of 8 x 10(-3) to 3 x 10(-4). Dpo4 is distributive but at high enzyme to template ratios can synthesize long stretches of DNA and can substitute for Taq polymerase in PCR. On damaged DNA templates, Dpo4 can facilitate translesion replication of an abasic site, a cis-syn thymine-thymine dimer, as well as acetyl aminofluorene adducted- and cisplatinated-guanine residues. Thus, although phylogenetically related to DinB polymerases, our studies suggest that the archaeal Dpo4 enzyme exhibits lesion-bypass properties that are, in fact, more akin to those of eukaryotic poleta.
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Affiliation(s)
- F Boudsocq
- Section on DNA Replication, Repair and Mutagenesis, National Institute of Child Health and Human Development, National Institutes of Health, MD 20892-2725, USA
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511
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Friedberg EC, Fischhaber PL, Kisker C. Error-prone DNA polymerases: novel structures and the benefits of infidelity. Cell 2001; 107:9-12. [PMID: 11595180 DOI: 10.1016/s0092-8674(01)00509-8] [Citation(s) in RCA: 106] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Studies on several recently discovered error-prone DNA polymerases reveal novel structures that may explain the low fidelity of this general class of enzymes, a number of which are involved in the replicative bypass (translesion synthesis) of base damage in DNA.
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Affiliation(s)
- E C Friedberg
- Laboratory of Molecular Pathology, Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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