Abstract
Template-dependent and template-independent nucleotidyl transfer reactions are fundamentally important in the maintenance of the genome as well as for gene expression in all organisms and viruses. These reactions are conserved and involve the condensation of an incoming nucleotide triphosphate at the 3′ hydroxyl of the growing oligonucleotide chain with concomitant release of pyrophosphate. DNA polymerase I (Pol I) isolated from E. coli extracts was initially characterized in in vitro reactions well over 50 years ago by the seminal work of Arthur Kornberg’s laboratory (Kornberg 1957; Lehman et al. 1958; Bessman et al. 1958). Inspired by this work, the discovery of a DNA-dependent RNA polymerase quickly followed in 1960 from a variety of researchers including Samuel Weiss (Weiss and Gladstone 1959), Jerald Hurwitz (Hurwitz et al. 1960), Audrey Stevens (Stevens 1960), and James Bonner (Huang et al. 1960). These early enzymatic characterizations of DNA-dependent deoxyribonucleotides and ribonucleotide incorporations gave credibility both to Watson and Crick’s DNA double helix model (Watson and Crick 1953) and the transcription operon model proposed by François Jacob and Jacques Monod (Jacob and Monod 1961).
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsAbbreviations
- CPD:
-
Cyclobutane pyrimidine dimers
- E. coli :
-
Escherichia coli
- FDX:
-
Fidaxomicin
- FILS:
-
Facial dysmorphism, immunodeficiency, livedo, and short statures
- kDa:
-
Kilodaltons
- pol:
-
Polymerase
- Pol I:
-
E. coli DNA polymerase I
- RdRp:
-
RNA-dependent RNA polymerase
- Rif:
-
Rifampicin
- rRNA:
-
Ribosomal RNA
- TLS:
-
Translesion synthesis
- UV:
-
Ultraviolet light
- XPD:
-
Xeroderma pigmentosum
References
Albertella MR, Lau A, O’Connor MJ (2005) The overexpression of specialized DNA polymerases in cancer. DNA Repair (Amst) 4(5):583–593
Allsopp RC, Harley CB (1995) Evidence for a critical telomere length in senescent human fibroblasts. Exp Cell Res 219(1):130–136
Armanios M (2009) Syndromes of telomere shortening. Annu Rev Genomics Hum Genet 10:45–61
Beese LS, Steitz TA (1991) Structural basis for the 3′-5′ exonuclease activity of Escherichia coli DNA polymerase I: a two metal ion mechanism. EMBO J 10(1):25–33
Beese LS, Derbyshire V, Steitz TA (1993) Structure of DNA polymerase I Klenow fragment bound to duplex DNA. Science 260(5106):352–355
Bessman MJ, Lehman IR, Simms ES, Kornberg A (1958) Enzymatic synthesis of deoxyribonucleic acid. II. General properties of the reaction. J Biol Chem 233(1):171–177
Bielas JH, Loeb KR, Rubin BP, True LD, Loeb LA (2006) Human cancers express a mutator phenotype. Proc Natl Acad Sci USA 103(48):18238–18242
Blanco L, Bernad A, Lazaro JM, Martin G, Garmendia C, Salas M (1989) Highly efficient DNA synthesis by the phage phi 29 DNA polymerase. Symmetrical mode of DNA replication. J Biol Chem 264(15):8935–8940
Bloom LB (2009) Loading clamps for DNA replication and repair. DNA Repair (Amst) 8(5):570–578
Braithwaite DK, Ito J (1993) Compilation, alignment, and phylogenetic relationships of DNA polymerases. Nucleic Acids Res 21(4):787–802
Burgers PM, Koonin EV, Bruford E, Blanco L, Burtis KC, Christman MF, Copeland WC, Friedberg EC, Hanaoka F, Hinkle DC, Lawrence CW, Nakanishi M, Ohmori H, Prakash L, Prakash S, Reynaud CA, Sugino A, Todo T, Wang Z, Weill JC, Woodgate R (2001) Eukaryotic DNA polymerases: proposal for a revised nomenclature. J Biol Chem 276(47):43487–43490
Dahlberg ME, Benkovic SJ (1991) Kinetic mechanism of DNA polymerase I (Klenow fragment): identification of a second conformational change and evaluation of the internal equilibrium constant. Biochemistry 30(20):4835–4843
Delucia AM, Chaudhuri S, Potapova O, Grindley ND, Joyce CM (2006) The properties of steric gate mutants reveal different constraints within the active sites of Y-family and A-family DNA polymerases. J Biol Chem 281(37):27286–27291
Goellner EM, Svilar D, Almeida KH, Sobol RW (2012) Targeting DNA polymerase as for therapeutic intervention. Curr Mol Pharmacol 5(1):68–87
Hirata A, Murakami KS (2009) Archaeal RNA polymerase. Curr Opin Struct Biol 19(6):724–731
Huang RC, Maheshwari N, Bonner J (1960) Enzymatic synthesis of RNA. Biochem Biophys Res Com 3(6):689–694
Hurwitz J, Bresler A, Diringer R (1960) The enzymic incorporation of ribonucleotides into polyribonucleotides and the effect of DNA. Biochem Biophys Res Com 3(1):15–19
Ishino Y, Komori K, Cann IKO, Koga Y (1998) A novel DNA polymerase family found in Archaea. J Bacteriol 180(8):2232–2236
Jacob F, Monod J (1961) Genetic regulatory mechanisms in the synthesis of proteins. J Mol Biol 3:318–356
Johnson KA (2010) The kinetic and chemical mechanism of high-fidelity DNA polymerases. Biochim Biophys Acta 1804(5):1041–1048
Johnson RE, Washington MT, Prakash S, Prakash L (2000) Fidelity of human DNA polymerase eta. J Biol Chem 275(11):7447–7450
Joyce CM, Potapova O, Delucia AM, Huang X, Basu VP, Grindley ND (2008) Fingers-closing and other rapid conformational changes in DNA polymerase I (Klenow fragment) and their role in nucleotide selectivity. Biochemistry 47(23):6103–6116
Jun SH, Reichlen MJ, Tajiri M, Murakami KS (2011) Archaeal RNA polymerase and transcription regulation. Crit Rev Biochem Mol Biol 46(1):27–40
Kamtekar S, Berman AJ, Wang J, Lazaro JM, de Vega M, Blanco L, Salas M, Steitz TA (2006) The phi29 DNA polymerase: protein-primer structure suggests a model for the initiation to elongation transition. EMBO J 25(6):1335–1343
Kornberg A (1957) Enzymatic synthesis of deoxyribonucleic acid. Harvey Lect 53:83–112
Kuchta RD, Benkovic P, Benkovic SJ (1988) Kinetic mechanism whereby DNA polymerase I (Klenow) replicates DNA with high fidelity. Biochemistry 27(18):6716–6725
Kunkel TA (2004) DNA replication fidelity. J Biol Chem 279(17):16895–16898
Lange SS, Takata K, Wood RD (2011) DNA polymerases and cancer. Nat Rev Cancer 11(2):96–110
Lehman IR, Bessman MJ, Simms ES, Kornberg A (1958) Enzymatic synthesis of deoxyribonucleic acid. I. Preparation of substrates and partial purification of an enzyme from Escherichia coli. J Biol Chem 233(1):163–170
Lemee F, Bergoglio V, Fernandez-Vidal A, Machado-Silva A, Pillaire MJ, Bieth A, Gentil C, Baker L, Martin AL, Leduc C, Lam E, Magdeleine E, Filleron T, Oumouhou N, Kaina B, Seki M, Grimal F, Lacroix-Triki M, Thompson A, Roche H, Bourdon JC, Wood RD, Hoffmann JS, Cazaux C (2010) DNA polymerase theta up-regulation is associated with poor survival in breast cancer, perturbs DNA replication, and promotes genetic instability. Proc Natl Acad Sci USA 107(30):13390–13395
Masutani C, Araki M, Yamada A, Kusumoto R, Nogimori T, Maekawa T, Iwai S, Hanaoka F (1999) Xeroderma pigmentosum variant (XP-V) correcting protein from HeLa cells has a thymine dimer bypass DNA polymerase activity. EMBO J 18(12):3491–3501
Moldovan GL, Pfander B, Jentsch S (2007) PCNA, the maestro of the replication fork. Cell 129(4):665–679
Nakamura T, Zhao Y, Yamagata Y, Hua YJ, Yang W (2012) Watching DNA polymerase eta make a phosphodiester bond. Nature 487(7406):196–201
Ohmori H, Friedberg EC, Fuchs RP, Goodman MF, Hanaoka F, Hinkle D, Kunkel TA, Lawrence CW, Livneh Z, Nohmi T, Prakash L, Prakash S, Todo T, Walker GC, Wang Z, Woodgate R (2001) The Y-family of DNA polymerases. Mol Cell 8(1):7–8
Ollis DL, Brick P, Hamlin R, Xuong NG, Steitz TA (1985) Structure of large fragment of Escherichia coli DNA polymerase I complexed with dTMP. Nature 313(6005):762–766
Pachlopnik Schmid J, Lemoine R, Nehme N, Cormier-Daire V, Revy P, Debeurme F, Debre M, Nitschke P, Bole-Feysot C, Legeai-Mallet L, Lim A, de Villartay JP, Picard C, Durandy A, Fischer A, de Saint BG (2012) Polymerase epsilon1 mutation in a human syndrome with facial dysmorphism, immunodeficiency, livedo, and short stature (“FILS syndrome”). J Exp Med 209(13):2323–2330
Starcevic D, Dalal S, Sweasy JB (2004) Is there a link between DNA polymerase beta and cancer? Cell Cycle 3(8):998–1001
Steitz TA (1993) DNA-dependent and RNA-dependent DNA-polymerases. Curr Opin Struct Biol 3(1):31–38
Steitz TA, Steitz JA (1993) A general two-metal-ion mechanism for catalytic RNA. Proc Natl Acad Sci USA 90(14):6498–6502
Stevens A (1960) Incorporation of the adenine ribonucleotide into RNA by cell fractions from, E. coli B. Biochem Biophys Res Com 3(1):92–96
Tan XH, Zhao M, Pan KF, Dong Y, Dong B, Feng GJ, Jia G, Lu YY (2005) Frequent mutation related with overexpression of DNA polymerase beta in primary tumors and precancerous lesions of human stomach. Cancer Lett 220(1):101–114
Trakselis MA, Benkovic SJ (2001) Intricacies in ATP-dependent clamp loading: variations across replication systems. Structure 9(11):999–1004
Watson JD, Crick FH (1953) Molecular structure of nucleic acids. Nature 171:737–738
Weiss SB, Gladstone L (1959) A mammalian system for the incorporation of cytidine triphosphate into ribonucleic acid. J Am Chem Soc 81(15):4118–4119
Weissbach A, Baltimore D, Bollum F, Gallo R, Korn D (1975) Nomenclature of eukaryotic DNA polymerases. Science 190(4212):401–402
Werner F, Grohmann D (2011) Evolution of multisubunit RNA polymerases in the three domains of life. Nat Rev Microbiol 9(2):85–98
Author information
Authors and Affiliations
Corresponding authors
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2014 Springer-Verlag Berlin Heidelberg
About this chapter
Cite this chapter
Trakselis, M.A., Murakami, K.S. (2014). Introduction to Nucleic Acid Polymerases: Families, Themes, and Mechanisms. In: Murakami, K., Trakselis, M. (eds) Nucleic Acid Polymerases. Nucleic Acids and Molecular Biology, vol 30. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-39796-7_1
Download citation
DOI: https://doi.org/10.1007/978-3-642-39796-7_1
Published:
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-39795-0
Online ISBN: 978-3-642-39796-7
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)