Abstract
DNA polymerase and DNA ligase are ubiquitous enzymes that synthesize complementary DNA strands according to the template DNA and ligate breaks in the backbone structure of DNA, respectively, in living organisms. Multiple enzymes have been identified from each organism, and the functional sharing of these enzymes has been investigated for both DNA polymerase and DNA ligase. In addition to their fundamental role in maintaining genome integrity during replication and repair, DNA polymerases and DNA ligases are widely used for genetic engineering techniques, including DNA cloning, dideoxy sequencing, DNA labeling, mutagenesis, and other in vitro DNA manipulations. Thermostable DNA polymerases and DNA ligases are especially important in PCR and LDR/LCR, which are indispensable techniques for gene manipulation. In this chapter, we have summarized the recent developments in DNA polymerases and DNA ligases from thermophilic microbes.
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References
Abravaya K, Carrino JJ, Muldoon S, Lee HH (1995) Nucleic Acids Res 23:675–682
Amann RI, Ludwig W, Schleifer KH (1995) Microbiol Rev 59:143–169
Ansorge WJ (2009) New Biotechnol 25:195–203
Baar C, d’Abbadie M, Vaisman A, Arana ME, Hofreiter M, Woodgate R, Kunkel TA, Holliger P (2011) Nucleic Acids Res 39:e51
Barany F (1991a) PCR Methods Appl 1:5–16
Barany F (1991b) Proc Natl Acad Sci USA 88:189–193
Barnes WM (1994) Proc Natl Acad Sci USA 91:2216–2220
Benarroch D, Shuman S (2006) Virology 353:133–143
Benjamin BD, Connolly BA (2004) Nucleic Acids Res 32:e176
Berquist BR, DasSarma P, DasSarma S (2007) BMC Genet 8:31
Bezsudnova EY, Kovalchuk MV, Mardanov AV, Poliakov KM, Popov VO, Ravin NV, Skryabin KG, Smagin VA, Stekhanova TN, Tikhonova TV (2009) Acta Crystallogr Sect F Struct Biol Cryst Commun 65:368–371
Bocquier AA, Liu L, Cann IKO, Komori K, Kohda D, Ishino Y (2001) Curr Biol 11:452–456
Böhlke K, Pisani FM, Vorgias CE, Frey B, Sobek H, Rossi M, Antranikian G (2000) Nucleic Acids Res 28:3910–3917
Braithwaite DK, Ito J (1993) Nucleic Acids Res 21:787–802
Brakmann S (2005) Cell Mol Life Sci 62:2634–2646
Brochier-Armanet C, Boussau B, Gribaldo S, Forterre P (2008) Nat Rev Microbiol 6:245–252
Brötz-Oesterhelt H, Knezevic I, Bartel S, Lampe T, Warnecke-Eberz U, Ziegelbauer K, Häbich D, Labischinski H (2003) J Biol Chem 278:39435–39442
Cann I, Ishino Y (1999) Genetics 152:1249–1267
Cann I, Komori K, Toh H, Kanai S, Ishino Y (1998) Proc Natl Acad Sci USA 95:14250–14255
Cann I, Ishino S, Nomura N, Sako Y, Ishino Y (1999) J Bacteriol 181:5984–5992
Castrec B, Laurent S, Henneke G, Flament D, Raffin JP (2010) J Mol Biol 396:840–848
Chen B, Sysoeva TA, Chowdhury S, Guo L, Nixon BT (2009) FEBS J 276:807–815
Chien A, Edgar DB, Trela JM (1976) J Bacteriol 127:1550–1557
Connolly BA (2009) Biochem Soc Trans 37:65–68
d’Abbadie M, Hofreiter M, Caisman A, Loakes D, Gasparutto D, Cadet J, Woodgate R, Pääbo S, Holliger P (2007) Nat Biotechnol 25:939–943
Desogus G, Onesti S, Brick P, Rossi M, Pisani FM (1999) Nucleic Acids Res 27:4444–4450
Dionne I, Nookala RK, Jackson SP, Doherty AJ, Bell SD (2003) Mol Cell 11:275–282
Eckert KA, Kunkel TA (1991) Genome Res 1:17–24
Elkins JG, Podar M, Graham DE, Makarova KS, Wolf Y, Randau L, Hedlund BP, Brochier-Armanet C, Kunin V, Anderson I et al (2008) Proc Natl Acad Sci USA 105:8102–8107
Fernandez-Arrojo L, Guazzaroni M-E, Lopez-Cortes N, Beloqui A, Ferrer M (2010) Curr Opin Biotechnol 21:725–733
Ferrer M, Golyshina OV, Beloqui A, Böttger LH, Andreu JM, Polaina J, De Lacey AL, Trautwein AX, Timmis KN, Golyshin PN (2008) Proc Natl Acad Sci USA 105:8878–8883
Firbank SJ, Wardle J, Heslop P, Lewis RJ, Connolly BAJ (2008) Mol Biol 381:529–539
Fogg MG, Pearl LH, Conolly BA (2002) Nat Struct Biol 9:922–927
Franklin MC, Wang J, Steitz TA (2001) Cell 105:657–667
Ghadessy FJ, Ong JL, Holliger P (2001) Proc Natl Acad Sci USA 98:4552–4557
Ghadessy FJ, Ramsay N, Boudsocq F, Loakes D, Brown A, Iwai S, Vaisman A, Woodgate R, Holliger P (2004) Nat Biotechnol 22:755–779
Gibbs MD, Reeves RA, Mandelman D, Mi Q, Lee J, Bergquist PL (2009) Extremophiles 13:817–826
Grúz P, Pisani FM, Shimizu M, Yamada M, Hayashi I, Morikawa K, Nohmi T (2001) J Biol Chem 276:47394–47401
Gueguen Y, Rolland JL, Lecompte O, Azam P, Le Romancer G, Flament D, Raffin JP, Dietrich J (2001) Eur J Biochem 268:5961–5969
Guo C, Kosarek-Stancel JN, Tang TS, Friedberg EC (2009) Cell Mol Life Sci 66:2363–2381
Hansen C, Wu L, Fox JD, Arezi B, Hogrefe HH (2011) Nucleic Acids Res 39:1801–1810
Hashimoto H, Nishioka M, Fujiwara S, Takagi M, Imanaka T, Inoue T, Kai Y (2001) J Mol Biol 306:469–477
Henneke G, Flament D, Hübscher U, Querellou J, Raffin JP (2005) J Mol Biol 350:53–64
Henry AA, Romesberg FE (2005) Curr Opin Biotechnol 16:370–377
Holmberg RC, Henry AA, Romesberg FE (2005) Biomol Eng 22:39–49
Housby JN, Southern EM (2002) Anal Biochem 302:88–94
Imamura M, Uemori T, Kato I, Ishino Y (1995) Biol Pharm Bull 18:1647–1652
Imanaka T (2011) In: Horikoshi K, Antranikian G, Bull AT, Robb FT, Stetter KO (eds) Extremophiles handbook, vol 1. Springer, Tokyo/Dordrecht/Heidelberg/London/New York, pp 475–495
Ishino Y, Cann I (1998) Genes Genet Syst 73:323–336
Ishino Y, Ishino S (2001) Method Enzymol 334:249–260
Ishino Y, Ishino S (2006) Nucleosides Nucleotides Nucleic Acids 25:681–691
Ishino S, Kawamura A, Ishino Y (2012) J Jpn Soc Extremophiles 11:19–25
Ishino Y, Ueno T, Miyagi M, Uemori T, Imamura M, Tsumasawa S, Kato I (1994) J Biochem 116:1019–1024
Ishino Y, Tsurimoto T, Ishino S, Cann I (2001) Genes Cells 6:699–706
Ito N, Nureki O, Shirouzu M, Yokoyama S, Hanaoka F (2003) Genes Cells 8:913–923
Ito N, Matsui I, Matsui E (2007) FEBS J 274:1340–1351
Jackson BR, Noble C, Lavesa-Curto M, Bond PL, Bowater RP (2007) Extremophiles 11:315–327
Jeon SJ, Ishikawa K (2003) FEBS Lett 550:69–73
Jeon HJ, Shin HJ, Choi JJ, Hoe HS, Kim HK, Suh SW, Kwon ST (2004) FEMS Microbiol Lett 237:111–118
Jokela M, Eskelinen A, Pospiech H, Rouvinen J, Syvaoja JE (2004) Nucleic Acids Res 32:2430–2440
Joyce CM, Steitz TA (1994) Annu Rev Biochem 63:777–822
Kennedy J, Flemer B, Jackson SA, Lejon DPH, Morrissey JP, O’Gara F, Dobson ADW (2010) Mar Drugs 8:608–628
Keppetipola N, Shuman S (2005) J Bacteriol 187:6902–6908
Kermekchiev MB, Tzekov A, Barnes WM (2003) Nucleic Acids Res 31:6139–6147
Kermekchiev MB, Kirilova LI, Vail EE, Barnes WM (2009) Nucleic Acids Res 37:e40
Kim YJ, Lee HS, Bae SS, Jeon JH, Yang SH, Lim JK, Kang SG, Kwon ST, Lee JH (2006) Biotechnol Lett 28:401–407
Kirk BW, Kuchta RD (1999) Biochemistry 38:7727–7736
Kiyonari S, Takayama K, Nishida H, Ishino Y (2006) J Biol Chem 281:28023–28032
Kiyonari S, Kamigochi T, Ishino Y (2007) Extremophiles 11:675–684
Kletzin A (1992) Nucleic Acids Res 20:5389–5396
Komori K, Ishino Y (2000) Protein Eng 13:41–47
Lai X, Shao H, Hao F, Huang L (2002) Extremophiles 6:469–477
Lao-Sirieix SH, Bell SD (2004) J Mol Biol 344:1251–1263
Lao-Sirieix SH, Nookala RK, Roversi P, Bell SD, Pellegrini L (2005) Nat Struct Mol Biol 12:1137–1144
Lauer G, Rudd EA, McKay DL, Ally A, Ally D, Backman KC (1991) J Bacteriol 173:5047–5053
Lawyer FC, Stoffel S, Saiki RK, Myambo K, Drummond R, Gelfand DH (1989) J Biol Chem 264:6427–6437
Le Breton M, Henneke G, Norais C, Flament D, Myllykallio H, Querellou J, Raffin JP (2007) J Mol Biol 374:1172–11785
Lee JY, Chang C, Song HK, Moon J, Yang JK, Kim HK, Kwon ST, Suh SW (2000) EMBO J 19:1119–1129
Lim JH, Choi J, Han SJ, Kim SH, Hwang HZ, Jin DK, Ahn BY, Han YS (2001) Extremophiles 5:161–168
Lin L-J, Yoshinaga A, Lin Y, Guzman C, Chen Y-H, Mei S, Lagunas AM, Koike S, Iwai S, Spies MA, Nair SK, Mackie RI, Ishino Y, Cann IKO (2010) J Mol Biol 397:13–30
Ling H, Boudsocq F, Woodgate R, Yang W (2001) Cell 107:91–102
Lipps G (2004) Biochem Soc Trans 32:240–244
Lipps G (2009) Biochem Soc Trans 37:42–45
Lipps G, Röther S, Hart C, Krauss G (2003) EMBO J 22:2516–2525
Lipps G, Weinzierl AO, von Scheven G, Buchen C, Cramer P (2004) Nat Struct Mol Biol 11:157–162
Liu L, Komori K, Ishino S, Bocquier AA, Cann IKO, Kohda D, Ishino Y (2001) J Biol Chem 276:45484–45490
Loeb LA, Monnat RJ Jr (2008) Nat Rev Genet 9:594–604
Lundberg KS, Shoemaker DD, Adams MW, Short JM, Sorge JA, Mathur EJ (1991) Gene 108:1–6
Luo J, Bergstrom DE, Barany F (1996) Nucleic Acids Res 24:3071–3078
Matsui E, Nishio M, Yokoyama H, Harata K, Darnis S, Matsui I (2003) Biochemistry 42:14968–14976
Matsukawa H, Yamagami T, Kawarabayasi Y, Miyashita Y, Takahashi M, Ishino Y (2009) Genes Genet Syst 84:3–13
Matsumiya S, Ishino Y, Morikawa K (2000) Protein Sci 10:17–23
Matsumiya S, Ishino S, Ishino Y, Morikawa K (2002) Genes Cells 7:911–922
Matsumiya S, Ishino S, Ishino Y, Morikawa K (2003) Protein Sci 12:823–831
Matsunaga F, Norais C, Forterre P, Myllykallio H (2003) EMBO Rep 4:154–158
Mayanagi K, Kiyonari S, Saito M, Shirai T, Ishino Y, Morikawa K (2009) Proc Natl Acad Sci USA 106:4647–4652
Mayanagi K, Kiyonari S, Nishida H, Saito M, Kohda D, Ishino Y, Shirai T, Morikawa K (2011) Proc Natl Acad Sci USA 108:1845–1849
Meier TI, Yan D, Peery RB, McAllister KA, Zook C, Peng SB, Zhao G (2008) FEBS J 275:5258–5271
Metzker ML (2010) Nat Rev Genet 11:31–45
Miesel L, Kravec C, Xin AT, McMonagle P, Ma S, Pichardo J, Feld B, Barrabee E, Palermo R (2007) Anal Biochem 366:9–17
Miyata T, Suzuki H, Oyama T, Mayanagi K, Ishino Y, Morikawa K (2005) Proc Natl Acad Sci USA 102:13795–13800
Motz M, Kober I, Girardot C, Loeser E, Bauer U, Albers M, Moeckel G, Minch E, Voss H, Kilger C, Koeg M (2002) J Biol Chem 277:16179–16188
Myers TW, Gelfand DH (1991) Biochemistry 30:7661–7666
Nakatani M, Ezaki S, Atomi H, Imanaka T (2000) J Bacteriol 182:6424–6433
Nishida H, Kiyonari S, Ishino Y, Morikawa K (2006) J Mol Biol 360:956–967
Nishida H, Mayanagi K, Kiyonari S, Sato Y, Oyama T, Ishino Y, Morikawa K (2009) Proc Natl Acad Sci USA 106:20693–20698
Nørholm MH (2010) BMC Biotechnol 10:21
Nunoura Y, Takaki Y, Kakuta J, Nishi S, Sugahara J, Kazuma H, Chee G-J, Hattori M, Kanai A, Atomi H, Takai K, Takami H (2011) Nucleic Acids Res 39:3204–3223
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) Mol Cell 8:7–8
Ong JL, Loakes D, Jaroslawski S, Too K, Holliger P (2006) J Mol Biol 361:537–550
Pascal MJ (2008) Curr Opin Struct Biol 18:96–105
Pascal JM, O’Brien PJ, Tomkinson AE, Ellenberger T (2004) Nature 432:473–478
Pascal JM, Tsodikov OV, Hura GL, Song W, Cotner EA, Classen S, Tomkinson AE, Tainer JA, Ellenberger T (2006) Mol Cell 24:279–291
Perler FB (2002) Nucleic Acids Res 30:383–384
Perler FB, Comb DG, Jack WE, Moran LS, Qiang B, Kucera RB, Benner J, Slatko BE, Nwankwo DO, Hempstead SK, Carow CKS, Jannasch H (1992) Proc Natl Acad Sci USA 89:5577–5581
Perler FB, Kumar S, Kong H (1996) Adv Protein Chem 48:377–435
Phang SM, Teo CY, Lo E, Wong VW (1995) Gene 163:65–68
Poidevin L, MacNeill SA (2006) BMC Mol Biol 7:44
Psifidi A, Dovas C, Banos G (2011) PLoS One 6:e14560
Rolland JL, Gueguen Y, Persillon C, Masson JM, Dietrich J (2004) FEMS Microbiol Lett 236:267–273
Rothwell PJ, Waksman G (2005) Adv Protein Chem 71:401–439
Saiki RR, Gelfand DH, Stoffel S, Scharf SJ, Higuchi R, Horn GT, Mullis KB, Erlich HA (1988) Science 239:487–491
Schleper C, Swanson RV, Mathur EJ, DeLong EF (1997) J Bacteriol 179:7803–7811
Seo MS, Kim YJ, Choi JJ, Lee MS, Kim JH, Lee JH, Kwon ST (2007) J Biotechnol 128:519–530
Shamoo Y, Steitz TA (1999) Cell 99:155–166
Shark KB, Conway T (1992) FEMS Microbiol Lett 75:19–26
Shen Y, Musti K, Hiramoto M, Kikuchi H, Kawarabayashi Y, Matsui I (2001) J Biol Chem 276:27376–27383
Shen Y, Tang X, Matsui I (2003) J Biol Chem 278:21247–21257
Shendure JS, Ji H (2008) Nat Biotechnol 26:1135–1145
Shuman S (2009) J Biol Chem 284:17365–17369
Silvian LF, Toth EA, Pham P, Goodman MF, Ellenberger T (2001) Nat Struct Biol 8:984–989
Singleton MR, Håkansson K, Timson DJ, Wigley DB (1999) Structure 7:35–42
Soler N, Marguet E, Cortez D, Desnoues N, Keller J, van Tilbeurgh H, Sezonov G, Forterre P (2010) Nucleic Acids Res 38:5088–5104
Sriskanda V, Kelman Z, Hurwitz J, Shuman S (2000) Nucleic Acids Res 28:2221–2228
Srivastava SK, Dube D, Tewari N, Dwivedi N, Tripathi RP, Ramachandran R (2005) Nucleic Acids Res 33:7090–7101
Srivastava SK, Dube D, Kukshal V, Jha AK, Hajela K, Ramachandran R (2007) Proteins 69:97–111
Sun Y, Seo MS, Kim JH, Kim YJ, Kim GA, Lee JI, Lee JH, Kwon ST (2008) Environ Microbiol 10:3212–3224
Suzuki M, Avicola AK, Hood L, Loeb LA (1997) J Biol Chem 272:11228–11235
Suzuki M, Yoshida S, Adman ET, Blank A, Loeb LA (2000) J Biol Chem 275:32728–32735
Tabor S, Richardson CC (1995) Proc Natl Acad Sci USA 92:6339–6343
Tahirov TH, Makarova KS, Rogozin IB, Pavlov YI, Koonin EV (2009) Biol Direct 4:11
Takagi M, Nishioka M, Kakihara H, Kitabayashi M, Inoue H, Kawakami B, Oka M, Imanaka T (1997) Appl Environ Microbiol 63:4504–4510
Takahashi M, Yamaguchi E, Uchida T (1984) J Biol Chem 259:10041–10047
Tang XF, Shen Y, Matsui E, Matsui I (2004) Biochemistry 43:11818–11827
Thorbjarnardóttir SH, Jónsson ZO, Andrésson OS, Kristjánsson JK, Eggertsson G, Palsdottir A (1995) Gene 8:1–6
Timson DJ, Wigley DB (1999) J Mol Biol 285:73–83
Tomkinson AE, Vijayakumar S, Pascal JM, Ellenberger T (2006) Chem Rev 106:687–699
Tong J, Cao W, Barany F (1999) Nucleic Acids Res 27:788–794
Tong J, Barany F, Cao W (2000) Nucleic Acids Res 28:1447–1454
Tori K, Kimizu M, Ishino S, Ishino Y (2007) J Bacteriol 189:5652–5657
Tosaka A, Ogawa M, Yoshida S, Suzuki M (2001) J Biol Chem 276:27562–27567
Uemori T, Ishino Y, Fujita K, Asada K, Kato I (1993a) J Biochem 113:401–410
Uemori T, Ishino Y, Toh H, Asada K, Kato I (1993b) Nucleic Acids Res 21:259–265
Uemori T, Ishino Y, Doi H, Kato I (1995) J Bacteriol 177:2164–2177
Uemori T, Sato Y, Kato I, Doi H, Ishino Y (1997) Genes Cells 2:499–512
Villbrandt B, Sobek H, Frey B, Schaumburg D (2000) Protein Eng 13:645–654
Vivona JB, Kelman Z (2003) FEBS Lett 546:167–172
Wang Y, Prosen DE, Mei L, Sullivan JC, Finney M, Vander Horn PB (2004) Nucleic Acids Res 32:1197–1207
Warbrick FM (2000) Bioessays 22:997–1006
Wardle J, Burgers PM, Cann IK, Darley K, Heslop P, Johansson E, Lin LJ, McGlynn P, Sanvoisin J, Stith CM, Connolly BA (2008) Nucleic Acids Res 36:705–711
Wilkinson A, Day J, Bowater R (2001) Mol Microbiol 40:1241–1248
Xu MQ, Southworth MW, Mersha FB, Hornstra LJ, Perler FB (1993) Cell 75:1371–1377
Yang W (2003) Curr Opin Struct Biol 13:23–30
Yang J, Li Z, Liu C, Cheng Y (2010) Chem Commun 46:2432–2434
Zhao A, Gray FC, MacNeill SA (2006) Mol Microbiol 59:743–752
Zhou BL, Pata JD, Steitz TA (2001) Mol Cell 8:427–437
Zillig W, Kletzin A, Schleper C, Holz I, Janekovic D, Hain J, Lanzendoerfer M, Kristjansson JK (1994) Syst Appl Microbiol 16:609–628
Zirvi M, Bergstrom DE, Saurage AS, Hammer RP, Barany F (1999) Nucleic Acids Res 27:e41
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Ishino, S., Ishino, Y. (2013). DNA Polymerases and DNA Ligases. In: Satyanarayana, T., Littlechild, J., Kawarabayasi, Y. (eds) Thermophilic Microbes in Environmental and Industrial Biotechnology. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-5899-5_17
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