Review

Effect of different divalent cations on the kinetics and fidelity of DNA polymerases

  • Received: 17 September 2018 Accepted: 23 November 2018 Published: 11 December 2018
  • DNA polymerases (DNA pols) are essential for accurately copying genomes of all organisms. The polymerase and exonuclease activities associated with DNA pols require the presence of two divalent cations which occupy the A and B metal ion sites. Even though the two-metal ion mechanism is generally applicable for all DNA pols, a third metal ion was proposed to be essential for phosphoryl transfer reaction. The metal ion in the A site is coordinated by six ligands including the 3′ hydroxyl group of the primer, the carboxylates of two aspartic acid residues, as well as water molecules and the metal ion exhibits a distorted octahedral geometry. This metal ion plays a crucial role in lowering the pKa of the 3′ hydroxyl group of the primer increasing its nucleophilicity for attack on α phosphorous atom of the incoming dNTP. The metal ion occupying the B site stabilizes the transition state and is coordinated to the non-bridging oxygen atoms of the incoming dNTP and carboxylates of aspartic acid residues along with carboxyl oxygen of an adjacent peptide bond. In a similar fashion, two divalent cations are required for the 3′–5′ exonuclease activity of DNA pols. Analogous to their role in the polymerase active site, one divalent cation lowers the pKa of the water molecule making it a more potent nucleophile and the other cation helps to stabilize the transition state, assisting in excision of the 3′ terminal nucleotide. These divalent cations affect the various fidelity checkpoints along minimal kinetic scheme for DNA pols. The effect of different divalent cations on various steps in the kinetic scheme, including their influence on ground-state binding affinity, base selectivity, efficiency of extension past a mismatch and the exonuclease activity are discussed. We have also attempted to explain why only certain divalent cations act as cofactors for various DNA pols based on their properties including ionic radii, coordination geometry, and their ability to lower the pKa of the 3′ hydroxyl group of primer strand.

    Citation: Ashwani Kumar Vashishtha, William H. Konigsberg. Effect of different divalent cations on the kinetics and fidelity of DNA polymerases[J]. AIMS Biophysics, 2018, 5(4): 272-289. doi: 10.3934/biophy.2018.4.272

    Related Papers:

  • DNA polymerases (DNA pols) are essential for accurately copying genomes of all organisms. The polymerase and exonuclease activities associated with DNA pols require the presence of two divalent cations which occupy the A and B metal ion sites. Even though the two-metal ion mechanism is generally applicable for all DNA pols, a third metal ion was proposed to be essential for phosphoryl transfer reaction. The metal ion in the A site is coordinated by six ligands including the 3′ hydroxyl group of the primer, the carboxylates of two aspartic acid residues, as well as water molecules and the metal ion exhibits a distorted octahedral geometry. This metal ion plays a crucial role in lowering the pKa of the 3′ hydroxyl group of the primer increasing its nucleophilicity for attack on α phosphorous atom of the incoming dNTP. The metal ion occupying the B site stabilizes the transition state and is coordinated to the non-bridging oxygen atoms of the incoming dNTP and carboxylates of aspartic acid residues along with carboxyl oxygen of an adjacent peptide bond. In a similar fashion, two divalent cations are required for the 3′–5′ exonuclease activity of DNA pols. Analogous to their role in the polymerase active site, one divalent cation lowers the pKa of the water molecule making it a more potent nucleophile and the other cation helps to stabilize the transition state, assisting in excision of the 3′ terminal nucleotide. These divalent cations affect the various fidelity checkpoints along minimal kinetic scheme for DNA pols. The effect of different divalent cations on various steps in the kinetic scheme, including their influence on ground-state binding affinity, base selectivity, efficiency of extension past a mismatch and the exonuclease activity are discussed. We have also attempted to explain why only certain divalent cations act as cofactors for various DNA pols based on their properties including ionic radii, coordination geometry, and their ability to lower the pKa of the 3′ hydroxyl group of primer strand.


    加载中
    [1] Echols H, Goodman MF (1991) Fidelity mechanisms in DNA replication. Annu Rev Biochem 60: 477–511. doi: 10.1146/annurev.bi.60.070191.002401
    [2] Johnson KA (1993) Conformational coupling in DNA polymerase fidelity. Annu Rev Biochem 62: 685–713. doi: 10.1146/annurev.bi.62.070193.003345
    [3] Joyce CM, Benkovic SJ (2004) DNA polymerase fidelity: kinetics, structure, and checkpoints. Biochemistry 43: 14317–14324. doi: 10.1021/bi048422z
    [4] Kunkel T, Bebenek K (1988) Recent studies of the fidelity of DNA synthesis. BBA-Gene Struct Expr 951: 1–15. doi: 10.1016/0167-4781(88)90020-6
    [5] Kunkel TA, Bebenek K (2000) DNA replication fidelity. Annu Rev Biochem 69: 497–529. doi: 10.1146/annurev.biochem.69.1.497
    [6] Drake JW (1969) Comparative rates of spontaneous mutation. Nature 221: 1132. doi: 10.1038/2211132a0
    [7] Goodman MF, Tippin B (2000) The expanding polymerase universe. Nat Rev Mol Cell Biol 1: 101–109.
    [8] Filee J, Forterre P, Sen-Lin T, et al. (2002) Evolution of DNA polymerase families: evidences for multiple gene exchange between cellular and viral proteins. J Mol Evol 54: 763–773. doi: 10.1007/s00239-001-0078-x
    [9] Vashishtha AK, Kuchta RD (2016) Effects of acyclovir, foscarnet, and ribonucleotides on Herpes Simplex Virus-1 DNA Polymerase: Mechanistic insights and a novel mechanism for preventing stable incorporation of ribonucleotides into DNA. Biochemistry 55: 1168–1177. doi: 10.1021/acs.biochem.6b00065
    [10] Vashishtha AK, Kuchta RD (2015) Polymerase and exonuclease activities in herpes simplex virus type 1 DNA polymerase are not highly coordinated. Biochemistry 54: 240–249. doi: 10.1021/bi500840v
    [11] Xia S, Wang M, Blaha G, et al. (2011) Structural insights into complete metal ion coordination from ternary complexes of B family RB69 DNA polymerase. Biochemistry 50: 9114–9124. doi: 10.1021/bi201260h
    [12] Snow ET, Xu LS, Kinney PL (1993) Effects of nickel ions on polymerase activity and fidelity during DNA replication in vitro. Chem Biol Interact 88: 155–173. doi: 10.1016/0009-2797(93)90089-H
    [13] Vaisman A, Ling H, Woodgate R, et al. (2005) Fidelity of Dpo4: effect of metal ions, nucleotide selection and pyrophosphorolysis. EMBO J 24: 2957–2967. doi: 10.1038/sj.emboj.7600786
    [14] Pelletier H, Sawaya MR, Wolfle W, et al. (1996) A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta. Biochemistry 35: 12762–12777. doi: 10.1021/bi9529566
    [15] Irimia A, Loukachevitch LV, Eoff RL, et al. (2010) Metal-ion dependence of the active-site conformation of the translesion DNA polymerase Dpo4 from Sulfolobus sulfataricus. Acta Crystallogr Sect F Struct Biol Commun 66: 1013–1018. doi: 10.1107/S1744309110029374
    [16] Sirover MA, Dube DK, Loeb LA (1979) On the fidelity of DNA replication. Metal activation of Escherichia coli DNA polymerase I. J Biol Chem 254: 107–111.
    [17] Sirover MA, Loeb LA (1977) On the fidelity of DNA replication. Effect of metal activators during synthesis with avian myeloblastosis virus DNA polymerase. J Biol Chem 252: 3605–3610.
    [18] Miyaki M, Murata I, Osabe M, et al. (1977) Effect of metal cations on misincorporation by E. coli DNA polymerases. Biochem Biophys Res Commun 77: 854–860. doi: 10.1016/S0006-291X(77)80056-9
    [19] Goodman MF, Keener S, Guidotti S, et al. (1983) On the enzymatic basis for mutagenesis by manganese. J Biol Chem 258: 3469–3475.
    [20] Sirover MA, Loeb LA (1976) Infidelity of DNA synthesis in vitro: screening for potential metal mutagens or carcinogens. Science 194: 1434–1436. doi: 10.1126/science.1006310
    [21] Lee HR, Wang M, Konigsberg W (2009) The reopening rate of the fingers domain is a determinant of base selectivity for RB69 DNA polymerase. Biochemistry 48: 2087–2098. doi: 10.1021/bi8016284
    [22] Villani G, Tanquy Le Gac N, Wasungu L, et al. (2002) Effect of manganese on in vitro replication of damaged DNA catalyzed by the herpes simplex virus type-1 DNA polymerase. Nucleic Acids Res 30: 3323–3332. doi: 10.1093/nar/gkf463
    [23] Xia S, Konigsberg WH (2014) RB69 DNA polymerase structure, kinetics, and fidelity. Biochemistry 53: 2752–2767. doi: 10.1021/bi4014215
    [24] Beard WA, Wilson SH (2014) Structure and mechanism of DNA polymerase β. Biochemistry 53: 2768–2780. doi: 10.1021/bi500139h
    [25] Sobol RW, Wilson SH (2001) Mammalian DNA beta-polymerase in base excision repair of alkylation damage. Prog Nucleic Acid Res Mol Biol 68: 57–74. doi: 10.1016/S0079-6603(01)68090-5
    [26] Beard WA, Wilson SH (2000) Structural design of a eukaryotic DNA repair polymerase: DNA polymerase beta. Mutat Res 460: 231–244. doi: 10.1016/S0921-8777(00)00029-X
    [27] Yang L, Arora K, Beard WA, et al. (2004) Critical role of magnesium ions in DNA polymerase beta's closing and active site assembly. J Am Chem Soc 126: 8441–8453. doi: 10.1021/ja049412o
    [28] Bakhtina M, Lee S, Wang Y, et al. (2005) Use of viscogens, dNTPalphaS, and rhodium(III) as probes in stopped-flow experiments to obtain new evidence for the mechanism of catalysis by DNA polymerase beta. Biochemistry 44: 5177–5187. doi: 10.1021/bi047664w
    [29] Nakamura T, Zhao Y, Yamagata Y, et al. (2012) Watching DNA polymerase eta make a phosphodiester bond. Nature 487: 196–201. doi: 10.1038/nature11181
    [30] Gao Y, Yang W (2016) Capture of a third Mg2+ is essential for catalyzing DNA synthesis. Science 352:1334–1337. doi: 10.1126/science.aad9633
    [31] Freudenthal BD, Beard WA, Shock DD, et al. (2013) Observing a DNA polymerase choose right from wrong. Cell 154: 157–168. doi: 10.1016/j.cell.2013.05.048
    [32] Xia S, Wang J, Konigsberg WH (2013) DNA mismatch synthesis complexes provide insights into base selectivity of a B family DNA polymerase. J Am Chem Soc 135: 193–202. doi: 10.1021/ja3079048
    [33] Doublie S, Tabor S, Long AM, et al. (1998) Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 A resolution. Nature 391: 251–258.
    [34] Johnson SJ, Taylor JS, Beese LS (2003) Processive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations. Proc Natl Acad Sci USA 100: 3895–3900. doi: 10.1073/pnas.0630532100
    [35] Johnson SJ, Beese LS (2004) Structures of mismatch replication errors observed in a DNA polymerase. Cell 116: 803–816. doi: 10.1016/S0092-8674(04)00252-1
    [36] Vashishtha AK, Konigsberg WH (2016) Effect of Different Divalent Cations on the Kinetics and Fidelity of RB69 DNA Polymerase. Biochemistry 55: 2661–2670. doi: 10.1021/acs.biochem.5b01350
    [37] Tabor S, Richardson CC (1989) Effect of manganese ions on the incorporation of dideoxynucleotides by bacteriophage T7 DNA polymerase and Escherichia coli DNA polymerase I. Proc Natl Acad Sci USA 86: 4076–4080. doi: 10.1073/pnas.86.11.4076
    [38] Hori K, Mark DF, Richardson CC (1979) Deoxyribonucleic acid polymerase of bacteriophage T7. Characterization of the exonuclease activities of the gene 5 protein and the reconstituted polymerase. J Biol Chem 254: 11598–11604.
    [39] Kuchta RD, Mizrahi V, Benkovic PA, et al. (1987) Kinetic mechanism of DNA polymerase I (Klenow). Biochemistry 26: 8410–8417. doi: 10.1021/bi00399a057
    [40] Venkitaraman AR (1989) Use of modified T7 DNA polymerase (sequenase version 2.0) for oligonucleotide site-directed mutagenesis. Nucleic Acids Res 17: 3314.
    [41] Joyce CM (1989) How DNA travels between the separate polymerase and 3'-5'-exonuclease sites of DNA polymerase I (Klenow fragment). J Biol Chem 264: 10858–10866.
    [42] Irimia A, Zang H, Loukachevitch LV, et al. (2006) Calcium is a cofactor of polymerization but inhibits pyrophosphorolysis by the Sulfolobus solfataricus DNA polymerase Dpo4. Biochemistry 45: 5949–5956. doi: 10.1021/bi052511+
    [43] Sirover MA, Loeb LA (1976) Metal-induced infidelity during DNA synthesis. Proc Natl Acad Sci USA 73: 2331–2335. doi: 10.1073/pnas.73.7.2331
    [44] Sirover MA, Loeb LA (1976) Metal activation of DNA synthesis. Biochem Biophys Res Commun 70: 812–817. doi: 10.1016/0006-291X(76)90664-1
    [45] Seal G, Shearman CW, Loeb LA (1979) On the fidelity of DNA replication. Studies with human placenta DNA polymerases. J Biol Chem 254: 5229–5237.
    [46] Vashishtha AK, Konigsberg WH (2018) The effect of different divalent cations on the kinetics and fidelity of Bacillus stearothermophilus DNA polymerase. AIMS Biophys 5: 125–143. doi: 10.3934/biophy.2018.2.125
    [47] Zhang H, Cao W, Zakharova E, et al. (2007) Fluorescence of 2-aminopurine reveals rapid conformational changes in the RB69 DNA polymerase-primer/template complexes upon binding incorporati of matched deoxynucleoside triphosphates. Nucleic Acids Res 35: 6052–6062. doi: 10.1093/nar/gkm587
    [48] Hariharan C, Bloom LB, Helquist SA, et al. (2006) Dynamics of nucleotide incorporation: snapshots revealed by 2-aminopurine fluorescence studies. Biochemistry 45: 2836–2844. doi: 10.1021/bi051644s
    [49] Frey MW, Sowers LC, Millar DP, et al. (1995) The nucleotide analog 2-aminopurine as a spectroscopic probe of nucleotide incorporation by the Klenow fragment of Escherichia coli polymerase I and bacteriophage T4 DNA polymerase. Biochemistry 34: 9185–9192. doi: 10.1021/bi00028a031
    [50] Chin YE, Snow ET, Cohen MD, et al. (1994) The effect of divalent nickel (Ni2+) on in vitro DNA replication by DNA polymerase alpha. Cancer Res 54: 2337–2341.
    [51] Bock CW, Katz AK, Markham GD, et al. (1999) Manganese as a replacement for magnesium and zinc: Functional comparison of the divalent ions. J Am Chem Soc 121: 7360–7372. doi: 10.1021/ja9906960
    [52] Dube DK, Loeb LA (1975) Manganese as a mutagenic agent during in vitro DNA synthesis. Biochem Biophys Res Commun 67: 1041–1046. doi: 10.1016/0006-291X(75)90779-2
    [53] Jin YH, Clark AB, Slebos RJC, et al. (2003) Cadmium is a mutagen that acts by inhibiting mismatch repair. Nat Genet 34: 326–329. doi: 10.1038/ng1172
    [54] Hays H, Berdis AJ (2002) Manganese substantially alters the dynamics of translesion DNA synthesis. Biochemistry 41: 4771–4778. doi: 10.1021/bi0120648
    [55] Beckman RA, Mildvan AS, Loeb LA (1985) On the fidelity of DNA replication: manganese mutagenesis in vitro. Biochemistry 24: 5810–5817. doi: 10.1021/bi00342a019
    [56] Doetsch PW, Chan GL, Haseltine WA (1985) T4 DNA polymerase (3'–5') exonuclease, an enzyme for the detection and quantitation of stable DNA lesions: the ultraviolet light example. Nucleic Acids Res 13: 3285–3304. doi: 10.1093/nar/13.9.3285
    [57] Kunkel TA, Soni A (1988) Exonucleolytic proofreading enhances the fidelity of DNA synthesis by chick embryo DNA polymerase-gamma. J Biol Chem 263: 4450–4459.
    [58] Wang W, Hellinga HW, Beese LS (2011) Structural evidence for the rare tautomer hypothesis of spontaneous mutagenesis. Proc Natl Acad Sci USA 108: 17644–17648. doi: 10.1073/pnas.1114496108
    [59] Bebenek K, Pedersen LC, Kunkel TA (2011) Replication infidelity via a mismatch with Watson-Crick geometry. Proc Natl Acad Sci USA 108: 1862–1867. doi: 10.1073/pnas.1012825108
    [60] Harris VH, Smith CL, Cummins WJ, et al. (2003) The effect of tautomeric constant on the specificity of nucleotide incorporation during DNA replication: support for the rare tautomer hypothesis of substitution mutagenesis. J Mol Biol 326: 1389–1401. doi: 10.1016/S0022-2836(03)00051-2
    [61] Topal MD, Fresco JR (1976) Complementary base pairing and the origin of substitution mutations. Nature 263: 285–289. doi: 10.1038/263285a0
    [62] Vashishtha AK, Wang J, Konigsberg WH (2016) Different Divalent Cations Alter the Kinetics and Fidelity of DNA Polymerases. J Biol Chem 291: 20869–20875. doi: 10.1074/jbc.R116.742494
    [63] Xia S, Vashishtha A, Bulkley D, et al. (2012) Contribution of partial charge interactions and base stacking to the efficiency of primer extension at and beyond abasic sites in DNA. Biochemistry 51: 4922–4931. doi: 10.1021/bi300296q
    [64] Zhang Y, Baranovskiy AG, Tahirov ET (2016) Divalent ions attenuate DNA synthesis by human DNA polymerase alpha by changing the structure of the template/primer or by perturbing the polymerase reaction. DNA Repair 43:24–33. doi: 10.1016/j.dnarep.2016.05.017
    [65] Schmitt MW, Kennedy SR, Salk JJ, et al. (2012) Detection of ultra-rare mutations by next-generation sequencing. Proc Natl Acad Sci USA 109: 14508–14513. doi: 10.1073/pnas.1208715109
    [66] Frederico LA, Kunkel TA, Shaw BR (1990) A sensitive genetic assay for the detection of cytosine deamination: determination of rate constants and the activation energy. Biochemistry 29: 2532–2537.
    [67] Bebenek K, Kunkel TA (1995) Analyzing fidelity of DNA polymerase. Methods Enz 262 217–232.
    [68] Yasukawa K, Iida K, Okano H, et al. (2017) Next-generation sequencing-based analysis of reverse transcriptase fidelity. Biochem Biophys Res Commun 492: 147–153. doi: 10.1016/j.bbrc.2017.07.169
    [69] Ellefson JW, Gollihar J, Shroff R, et al. (2016) Synthetic evolutionary origin of a proofreading reverse transcriptase. Science 352: 1590–1593. doi: 10.1126/science.aaf5409
  • Reader Comments
  • © 2018 the Author(s), licensee AIMS Press. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0)
通讯作者: 陈斌, bchen63@163.com
  • 1. 

    沈阳化工大学材料科学与工程学院 沈阳 110142

  1. 本站搜索
  2. 百度学术搜索
  3. 万方数据库搜索
  4. CNKI搜索

Metrics

Article views(3890) PDF downloads(1724) Cited by(2)

Article outline

Figures and Tables

Figures(3)  /  Tables(2)

/

DownLoad:  Full-Size Img  PowerPoint
Return
Return

Catalog