Base excision repair in Archaea: Back to the future in DNA repair

DNA Repair

Volumn 21, Issue , 2014, Pages 148-157

  Grasso, Stefano ^a   Tell, Gianluca ^a  

^a UNIVERSITY OF UDINE   (Italy)

Author keywords

AP endonuclease; Archaea; Base excision repair; DNA repair; Glycosylase

Indexed keywords

DNA; DNA (APURINIC OR APYRIMIDINIC SITE) LYASE; DNA A; ENDONUCLEASE; FLAP ENDONUCLEASE; LIGASE; LYASE; URACIL DNA GLYCOSIDASE; ARCHAEAL PROTEIN; POLYDEOXYRIBONUCLEOTIDE SYNTHASE;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ARCHAEON; DEAMINATION; DNA BINDING MOTIF; DNA DAMAGE; DNA REPAIR; DNA REPLICATION; DNA SYNTHESIS; ENZYME ACTIVATION; ENZYME ACTIVITY; ENZYME MECHANISM; ENZYME METABOLISM; EXCISION REPAIR; HORIZONTAL GENE TRANSFER; IN VITRO STUDY; NONHUMAN; PRIORITY JOURNAL; RNA EDITING; SHORT SURVEY; THERMOSTABILITY; GENETICS; METABOLISM; MOLECULAR EVOLUTION;

BACTERIA (MICROORGANISMS); EUKARYOTA;

ARCHAEA; ARCHAEAL PROTEINS; DNA REPAIR; DNA REPAIR ENZYMES; EVOLUTION, MOLECULAR;

EID: 84907883265     PISSN: 15687864     EISSN: 15687856     Source Type: Journal    
DOI: 10.1016/j.dnarep.2014.05.006     Document Type: Review

References (106)

1. Woese C.R. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc. Natl. Acad. Sci. U.S.A. 1990, 87(12):4576-4579. 10.1073/pnas.87.12.4576.
2. Woese C.R., Fox G.E. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc. Natl. Acad. Sci. U.S.A. 1977, 74(11):5088-5090. 10.1073/pnas.74.11.5088.
3. Pace N.R. Time for a change. Nature 2006, 441(7091):289. 10.1038/441289a.
4. Mayr E. Two empires or three?. Proc. Natl. Acad. Sci. U.S.A. 1998, 95(17):9720-9723. 10.1073/pnas.95.17.9720.
5. Keeling P.J., Doolittle W.F. Archaea: narrowing the gap between prokaryotes and eukaryotes. Proc. Natl. Acad. Sci. U.S.A. 1995, 92(13):5761-5764.
6. Weinzierl R.O.J. The RNA polymerase factory and archaeal transcription. Chem. Rev. 2013, 8350-8376. 10.1021/cr400148k.
7. Decker K.B., Hinton D.M. Transcription regulation at the core: similarities among Bacterial, Archaeal, and Eukaryotic RNA polymerases. Annu. Rev. Microbiol. 2012, 67(1):113-139. 10.1146/annurev-micro-092412-155756.
8. Ishino Y., Ishino S. Rapid progress of DNA replication studies in Archaea, the third domain of life. Sci. China Life Sci. 2012, 55(5):386-403.
9. Kelman L.M., Kelman Z. Multiple origins of replication in archaea. Trends Microbiol. 2004, 12(9):399-401. 10.1016/j.tim.2004.07.001.
10. Watson J.D., Baker T.A., Bell S.P., Gann A., Levine M., Losick R. Molecular Biology of the Gene 2013, Benjamin Cummings, ISBN-10: 0321905377. 7th ed.
11. Grogan D.W. Stability and repair of DNA in hyperthermophilic Archaea. Curr. Issues Mol. Biol. 2004, 6(2):137-144. 10.1093/nar/gkl604.
12. Anderson I., Ulrich L.E., Lupa B., Susanti D., Porat I., Hooper S.D., Lykidis A., Sieprawska-Lupa M., Dharmarajan L., Goltsman E., et al. Genomic characterization of methanomicrobiales reveals three classes of methanogens. PLoS ONE 2009, 4(6):e5797. Ed. by N. Ahmed. 10.1371/journal.pone.0005797.
13. Eisen J.A. A phylogenomic study of the MutS family of proteins. Nucleic Acids Res. 1998, 26(18):4291-4300. 10.1093/nar/26.18.4291.
14. Kelman Z., White M.F. Archaeal DNA replication and repair. Curr. Opin. Microbiol. 2005, 8(6):669-676. 10.1016/j.mib.2005.10.001.
15. Yonekura S.-I., Nakamura N., Yonei S., Zhang-Akiyama Q.-M. Generation, biological consequences and repair mechanisms of cytosine deamination in DNA. J. Radiat. Res. (Tokyo) 2009, 50(1):19-26. 10.1269/jrr.08080.
16. Krokan H.E., Drabøs F., Slupphaug G. Uracil in DNA - occurrence, consequences and repair. Oncogene 2002, 21(58):8935-8948. 10.1038/sj.onc.1205996.
17. Lindahl T., Nyberg B. Heat-induced deamination of cytosine residues in deoxyribonucleic acid. Biochemistry 1974, 13(16):3405-3410. 10.1021/bi00713a035.
18. Koulis A., Cowan D.A., Pearl L.H., Savva R. Uracil-DNA glycosylase activities in hyperthermophilic micro-organisms. FEMS Microbiol. Lett. 1996, 143(2-3):267-271. 10.1111/j.1574-6968.1996.tb08491.x.
19. Jacobs K.L., Grogan D.W. Rates of spontaneous mutation in an archaeon from geothermal environments. J. Bacteriol. 1997, 179(10):3298-3303. 10.1007/s11427-012-4324-9.
20. Andersen S. Incorporation of dUMP into DNA is a major source of spontaneous DNA damage, while excision of uracil is not required for cytotoxicity of fluoropyrimidines in mouse embryonic fibroblasts. Carcinogenesis 2004, 26(3):547-555. 10.1093/carcin/bgh347.
21. Lindahl T. Instability and decay of the primary structure of DNA. Nature 1993, 362(6422):709-715. 10.1038/362709a0.
22. Friedberg E.C., Walker G.C., Siede W., Schultz R.A. DNA repair and mutagenesis 2006, ASM Press, ISBN 978-1-55581-319-2.
23. Sandigursky M., Franklin W.A. Uracil-DNA glycosylase in the extreme thermophile Archaeoglobus fulgidus. J. Biol. Chem. 2000, 275(25):19146-19149. 10.1074/jbc.M001995200.
24. Aravind L., Koonin E.V. The alpha/beta fold uracil DNA glycosylases: a common origin with diverse fates. Genome Biol. 2000, 1(4). RESEARCH0007. 10.1186/gb-2000-1-4-research0007.
25. Pearl L.H. Structure and function in the uracil-DNA glycosylase super-family. Mutat. Res./DNA Repair 2000, 460(3-4):165-181. 10.1016/S0921-8777(00)00025-2.
26. Varshney U., Hutcheon T., van de J.H., Sande Sequence analysis, expression, and conservation of Escherichia coli uracil DNA glycosylase and its gene (ung). J. Biol. Chem. 1988, 263(16):7776-7784.
27. Gallinari P., Jiricny J. A new class of uracil-DNA glycosylases related to human thymine-DNA glycosylase. Nature 1996, 383(6602):735-738. 10.1038/383735a0.
28. Lucas-Lledo J.I., Maddamsetti R., Lynch M. Phylogenomic analysis of the uracil-DNA glycosylase superfamily. Mol. Biol. Evol. 2011, 28(3):1307-1317. 10.1093/molbev/msq318.
29. Lee H.-W., Dominy B.N., Cao W. New family of deamination repair enzymes in uracil-DNA glycosylase superfamily. J. Biol. Chem. 2011, 286(36):31282-31287. 10.1074/jbc.M111.249524.
30. Begley T.J., Cunningham R.P. Methanobacterium thermoformicicum thymine DNA mismatch glycosylase: conversion of an N-glycosylase to an AP lyase. Protein Eng. 1999, 12(4):333-340. 10.1093/protein/12.4.333.
31. Back J., Chung J.H., Park Y.I., Kim K.S., Han Y.S. Endonuclease IV enhances base excision repair of endonuclease III from Methanobacterium thermoautotrophicum. DNA Repair 2003, 2(5):455-470. 10.1016/S1568-7864(02)00243-4.
32. Haushalter K.A., Todd Stukenberg P., Kirschner M.W., Verdine G.L. Identification of a new uracil-DNA glycosylase family by expression cloning using synthetic inhibitors. Curr. Biol. 1999, 9(4):174-185. 10.1016/S0960-9822(99)80087-6.
33. Sartori A.A. Biochemical characterization of uracil processing activities in the hyperthermophilic archaeon Pyrobaculum aerophilum. J. Biol. Chem. 2001, 276(32):29979-29986. 10.1074/jbc.M102985200.
34. Yang H., Fitz-Gibbon S., Marcotte E.M., Tai J.H., Hyman E.C., Miller J.H. Characterization of a thermostable DNA glycosylase specific for U/G and T/G mismatches from the hyperthermophilic archaeon Pyrobaculum aerophilum. J. Bacteriol. 2000, 182(5):1272-1279. 10.1128/JB.182.5.1272-1279.2000.
35. Sandigursky M., Franklin W.A. Thermostable uracil-DNA glycosylase from Thermotoga maritima a member of a novel class of DNA repair enzymes. Curr. Biol. 1999, 9(10):531-534. 10.1016/S0960-9822(99)80237-1.
36. Engstrom L.M., Partington O.A., David S.S. An iron-sulfur cluster loop motif in the Archaeoglobus fulgidus uracil-DNA glycosylase mediates efficient uracil recognition and removal. Biochemistry 2012, 51(25):5187-5197. 10.1021/bi3000462.
37. Dionne I., Bell S.D. Characterization of an archaeal family 4 uracil DNA glycosylase and its interaction with PCNA and chromatin proteins. Biochem. J. 2005, 387(Pt 3):859-863. 10.1042/BJ20041661.
38. Kiyonari S., Uchimura M., Shirai T., Ishino Y. Physical and functional interactions between uracil-DNA glycosylase and proliferating cell nuclear antigen from the euryarchaeon Pyrococcus furiosus. J. Biol. Chem. 2008, 283(35):24185-24193. 10.1074/jbc.M802837200.
39. Kiyonari S., Tahara S., Uchimura M., Shirai T., Ishino S., Ishino Y. Studies on the base excision repair (BER) complex in Pyrococcus furiosus. Biochem. Soc. Trans. 2009, 37(1):79. 10.1042/BST0370079.
40. Sartori A.A., Fitz-Gibbon S., Yang H., Miller J.H., Jiricny J. A novel uracil-DNA glycosylase with broad substrate specificity and an unusual active site. EMBO J. 2002, 21(12):3182-3191. 10.1093/emboj/cdf309.
41. Moen M.N., Knaevelsrud I., Haugland G.T., Grosvik K., Birkeland N.-K., Klungland A., Bjelland S. Uracil-DNA glycosylase of Thermoplasma acidophilum directs long-patch base excision repair, which is promoted by deoxynucleoside triphosphates and ATP/ADP, into short-patch repair. J. Bacteriol. 2011, 193(17):4495-4508. 10.1128/JB.00233-11.
42. Boiteux S., Radicella J.P. The human OGG1 gene: structure, functions, and its implication in the process of carcinogenesis. Arch. Biochem. Biophys. 2000, 377(1):1-8. 10.1006/abbi.2000.1773.
43. Matsumoto Y. Escherichia coli Nth and human hNTH1 DNA glycosylases are involved in removal of 8-oxoguanine from 8-oxoguanine/guanine mispairs in DNA. Nucleic Acids Res. 2001, 29(9):1975-1981. 10.1093/nar/29.9.1975.
44. Kazak L., Reyes A., Holt I.J. Minimizing the damage: repair pathways keep mitochondrial DNA intact. Nat. Rev. Mol. Cell Biol. 2012, 13(10):659-671. 10.1038/nrm3439.
45. Sobol R.W., Horton J.K., Kühn R., Gu H., Singhal R.K., Prasad R., Rajewsky K., Wilson S.H. Requirement of mammalian DNA polymerase-beta in base-excision repair. Nature 1996, 379(6561):183-186. 10.1038/379183a0.
46. Matsumoto Y., Kim K. Excision of deoxyribose phosphate residues by DNA polymerase beta during DNA repair. Science 1995, 269(5224):699-702. 10.1126/science.7624801.
47. Sartori A.A. Enzymology of base excision repair in the hyperthermophilic archaeon Pyrobaculum aerophilum. J. Biol. Chem. 2003, 278(27):24563-24576. 10.1074/jbc.M302397200.
48. Yang H., Phan I.T., Fitz-Gibbon S., Shivji M.K., Wood R.D., Clendenin W.M., Hyman E.C., Miller J.H. A thermostable endonuclease III homolog from the archaeon Pyrobaculum aerophilum. Nucleic Acids Res. 2001, 29(3):604-613. 10.1093/nar/29.3.604.
49. Knævelsrud I., Moen M.N., Grosvik K., Haugland G.T., Birkeland N.-K., Klungland A., Leiros I., Bjelland S. The hyperthermophilic euryarchaeon Archaeoglobus fulgidus repairs uracil by single-nucleotide replacement. J. Bacteriol. 2010, 192(21):5755-5766. 10.1128/JB.00135-10.
50. Chung J.H., Suh M.J., Park Y.I., Tainer J.A., Han Y.S. Repair activities of 8-oxoguanine DNA glycosylase from Archaeoglobus fulgidus, a hyperthermophilic archaeon. Mutat. Res. 2001, 486(2):99-111. 10.1016/S0921-8777(01)00081-7.
51. Shekhtman A., McNaughton L., Cunningham R.P., Baxter S.M. Identification of the Archaeoglobus fulgidus endonuclease III DNA interaction surface using heteronuclear NMR methods. Structure 1999, 7(8):919-930. 10.1016/S0969-2126(99)80119-1.
52. Chung J.H. A novel uracil-DNA glycosylase family related to the helix-hairpin-helix DNA glycosylase superfamily. Nucleic Acids Res. 2003, 31(8):2045-2055. 10.1093/nar/gkg319.
53. Schomacher L., Smolorz S., Ciirdaeva E., Ber S., Kramer W., Fritz H.-J. Helix-hairpin-helix protein MJ1434 from Methanocaldococcus jannaschii and EndoIV homologue TTC0482 from Thermus thermophilus HB27 do not process DNA uracil residues. Nucleic Acids Res. 2010, 38(15):5119-5129. 10.1093/nar/gkq270.
54. Hecker A., Graille M., Madec E., Gadelle D., Le Cam E., van Tilbergh H., Forterre P. The universal Kae1 protein and the associated Bud32 kinase (PRPK), a mysterious protein couple probably essential for genome maintenance in Archaea and Eukarya. Biochem. Soc. Trans. 2009, 37(Pt 1):29-35. 10.1042/BST0370029.
55. Wilson D., Barsky D. The major human abasic endonuclease: formation, consequences and repair of abasic lesions in DNA. Mutat. Res. 2001, 485(4):283-307. 10.1016/S0921-8777(01)00063-5.
56. Boiteux S., Guillet M. Abasic sites in DNA: repair and biological consequences in Saccharomyces cerevisiae. DNA Repair (Amst.) 2004, 3(1):1-12. 10.1016/j.dnarep.2003.10.002.
57. Tell G., Quadrifoglio F., Tiribelli C., Kelley M.R. The many functions of APE1/Ref-1: not only a DNA repair enzyme. Antioxid. Redox Signal. 2009, 11(3):601-620. 10.1089/ars.2008.2194.
58. Ishchenko A.A. Characterisation of new substrate specificities of Escherichia coli and Saccharomyces cerevisiae AP endonucleases. Nucleic Acids Res. 2003, 31(21):6344-6353. 10.1093/nar/gkg812.
59. Hegde M.L., Hazra T.K., Mitra S. Early steps in the DNA base excision/single-strand interruption repair pathway in mammalian cells. Cell Res. 2008, 18(1):27-47. 10.1038/cr.2008.8.
60. Schmiedel R., Kuettner E.B., Keim A., Sträter N., Greiner-Stöffele T. Structure and function of the abasic site specificity pocket of an AP endonuclease from Archaeoglobus fulgidus. DNA Repair 2009, 8(2):219-231. 10.1016/j.dnarep.2008.10.009.
61. Kiyonari S., Tahara S., Shirai T., Iwai S., Ishino S., Ishino Y. Biochemical properties and base excision repair complex formation of apurinic/apyrimidinic endonuclease from Pyrococcus furiosus. Nucleic Acids Res. 2009, 37(19):6439-6453. 10.1093/nar/gkp720.
62. Tsutakawa S.E., Lafrance-Vanasse J., Tainer J.A. The cutting edges in DNA repair, licensing, and fidelity: DNA and RNA repair nucleases sculpt DNA to measure twice, cut once. DNA Repair (Amst.) 2014, (Epub ahead of print). 10.1016/j.dnarep.2014.03.022.
63. Yasui A. Alternative excision repair pathways. Cold Spring Harb. Perspect. Biol. 2013, 5(6):a012617. 10.1101/cshperspect.a012617.
64. Kiyonari S., Egashira Y., Ishino S., Ishino Y. Biochemical characterization of endonuclease V from the hyperthermophilic archaeon, Pyrococcus furiosus. J. Biochem. 2014, 155(5):325-333. 10.1093/jb/mvu010.
65. Jobert L., Nilsen H. Regulatory mechanisms of RNA function: emerging roles of DNA repair enzymes. Cell. Mol. Life Sci. 2014, (Epub ahead of print). 10.1007/s00018-014-1562-y.
66. Kaneda K., Ohishi K., Sekiguchi J. Characterization of the AP endonucleases from Thermoplasma volcanium and Lactobacillus plantarum: contributions of two important tryptophan residues to AP site recognition. Biosci. Biotechnol. Biochem. 2006, 70(9):2213-2221. 10.1271/bbb.60153.
67. Lakomek K., Dickmanns A., Ciirdaeva E., Schomacher L., Ficner R. Crystal structure analysis of DNA uridine endonuclease Mth212 bound to DNA. J. Mol. Biol. 2010, 399(4):604-617. 10.1016/j.jmb.2010.04.044.
68. Georg J., Schomacher L., Chong J.P.J., Majernik A.I., Raabe M., Urlaub H., Muller S., Ciirdaeva E., Kramer W., Fritz H.-J. The Methanothermobacter thermautotrophicus ExoIII homologue Mth212 is a DNA uridine endonuclease. Nucleic Acids Res. 2006, 34(18):5325-5336.
69. Pfeifer S., Greiner-Stöffele T. A recombinant exonuclease III homologue of the thermophilic archaeon Methanothermobacter thermautotrophicus. DNA Repair 2005, 4(4):433-444. 10.1016/j.dnarep.2004.11.008.
70. Robertson A.B., Klungland A., Rognes T., Leiros I. DNA repair in mammalian cells. Cell. Mol. Life Sci. 2009, 66(6):981-993. 10.1007/s00018-009-8740-3.
71. Cann I.K., Ishino Y. Archaeal DNA replication: identifying the pieces to solve a puzzle. Genetics 1999, 152(4):1249-1267.
72. Schomacher L., Chong J.P.J., McDermott P., Kramer W., Fritz H.-J. DNA uracil repair initiated by the archaeal ExoIII homologue Mth212 via direct strand incision. Nucleic Acids Res. 2009, 37(7):2283-2293. 10.1093/nar/gkp102.
73. Schomacher L., Schürer K.A., Ciirdaeva E., McDermott P., Chong J.P., Kramer W., Fritz H.-J. Archaeal DNA uracil repair via direct strand incision: a minimal system reconstituted from purified components. DNA Repair 2010, 9(4):438-447. 10.1016/j.dnarep.2010.01.004.
74. Wardle J., Burgers P.M.J., Cann I.K.O., Darley K., Heslop P., Johansson E., Lin L.-J., McGlynn P., Sanvoisin J., Stith C.M., et al. Uracil recognition by replicative DNA polymerases is limited to the archaea, not occurring with bacteria and eukarya. Nucleic Acids Res. 2007, 36(3):705-711. 10.1093/nar/gkm1023.
75. Tahirov T.H., Makarova K.S., Rogozin I.B., Pavlov Y.I., Koonin E.V. Evolution of DNA polymerases: an inactivated polymerase-exonuclease module in Pol e{open} and a chimeric origin of eukaryotic polymerases from two classes of archaeal ancestors. Biol. Direct 2009, 4(1):11. 10.1186/1745-6150-4-11.
76. Le Breton M., Henneke G., Norais C., Flament D., Myllykallio H., Querellou J., Raffin J.-P. The heterodimeric primase from the euryarchaeon Pyrococcus abyssi: a multifunctional enzyme for initiation and repair?. J. Mol. Biol. 2007, 374(5):1172-1185. 10.1016/j.jmb.2007.10.015.
77. Pascal J.M., Tsodikov O.V., Hura G.L., Song W., Cotner E.A., Classen S., Tomkinson A.E., Tainer J.A., Ellenberger T. A flexible interface between DNA ligase and PCNA supports conformational switching and efficient ligation of DNA. Mol. Cell 2006, 24(2):279-291. 10.1016/j.molcel.2006.08.015.
78. Dionne I., Nookala R.K., Jackson S.P., Doherty A.J., Bell S.D. A heterotrimeric PCNA in the hyperthermophilic archaeon Sulfolobus solfataricus. Mol. Cell 2006, 11(1):275-282. 10.1016/S1097-2765(02)00824-9.
79. Kawai A., Hashimoto H., Higuchi S., Tsunoda M., Sato M., Nakamura K.T., Miyamoto S. A novel heterotetrameric structure of the crenarchaeal PCNA2-PCNA3 complex. J. Struct. Biol. 2011, 174(3):443-450. 10.1016/j.jsb.2011.02.006.
80. Winter J.A., Bunting K.A. Rings in the extreme: PCNA interactions and adaptations in the Archaea. Archaea 2012, 1-8. 10.1155/2012/951010.
81. Mase T., Kubota K., Miyazono K.-i., Kawarabayasi Y., Tanokura M. Structure of flap endonuclease 1 from the hyperthermophilic archaeon Desulfurococcus amylolyticus. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 2011, 67(2):209-213. 10.1107/S1744309110053030.
82. Matsui E., Musti K.V., Abe J., Yamasaki K., Matsui I., Harata K. Molecular structure and novel DNA binding sites located in loops of flap endonuclease-1 from Pyrococcus horikoshii. J. Biol. Chem. 2002, 277(40):37840-37847. 10.1074/jbc.M205235200.
83. Hosfield D.J., Mol C.D., Shen B., Tainer J.A. Structure of the DNA repair and replication endonuclease and exonuclease FEN-1. Cell 1998, 95(1):135-146. 10.1016/S0092-8674(00)81789-4.
84. Hwang K.Y., Baek K., Kim H.Y., Cho Y. The crystal structure of flap endonuclease-1 from Methanococcus jannaschii. Nat. Struct. Biol. 1998, 5(8):707-713. 10.1038/1406.
85. Chapados B.R., Hosfield D.J., Han S., Qiu J., Yelent B., Shen B., Tainer J.A. Structural basis for FEN-1 substrate specificity and PCNA-mediated activation in DNA replication and repair. Cell 2004, 116(1):39-50. 10.1016/S0092-8674(03)01036-5.
86. Lin Y., Guzman C.E., McKinney M.C., Nair S.K., Ha T., Cann I.K.O. Methanosarcina acetivorans Flap endonuclease 1 activity is inhibited by a cognate single-stranded-DNA-binding protein. J. Bacteriol. 2006, 188(17):6153-6167. 10.1128/JB.00045-06.
87. Roberts J.A. An archaeal endonuclease displays key properties of both eukaryal XPF-ERCC1 and Mus81. J. Biol. Chem. 2004, 280(7):5924-5928. 10.1074/jbc.M412766200.
88. Tomkinson A.E., Vijayakumar S., Pascal J.M., Ellenberger T. DNA ligases: structure, reaction mechanism, and function. Chem. Rev. 2006, 106(2):687-699. 10.1021/cr040498d.
89. Dianov G., Lindahl T. Reconstitution of the DNA base excision-repair pathway. Curr. Biol. 1994, 4(12):1069-1076. 10.1016/S0960-9822(00)00245-1.
90. Martin I.V., MacNeill S.A. ATP-dependent DNA ligases. Genome Biol. 2002, 3(4). REVIEWS3005. 10.1186/gb-2002-3-4-reviews3005.
91. Kletzin A. Molecular characterisation of a DNA ligase gene of the extremely thermophilic archaeon Desulfurolobus ambivalens shows close phylogenetic relationship to eukaryotic ligases. Nucleic Acids Res. 1992, 20(20):5389-5396. 10.1093/nar/20.20.5389.
92. Nakatani M., Ezaki S., Atomi H., Imanaka T. Substrate recognition and fidelity of strand joining by an archaeal DNA ligase. Eur. J. Biochem. 2002, 269(2):650-656. 10.1046/j.0014-2956.2001.02695.x.
93. Sriskanda V., Kelman Z., Hurwitz J., Shuman S. Characterization of an ATP-dependent DNA ligase from the thermophilic archaeon Methanobacterium thermoautotrophicum. Nucleic Acids Res. 2000, 28(11):2221-2228. 10.1128/JB.187.20.6902-6908.2005.
94. Lai X., Shao H., Hao F., Huang L. Biochemical characterization of an ATP-dependent DNA ligase from the hyperthermophilic crenarchaeon Sulfolobus shibatae. Extremophiles 2002, 6(6):469-477. 10.1007/s00792-002-0284-5.
95. Rolland J.-l., Gueguen Y., Persillon C., Masson J.-M., Dietrich J. Characterization of a thermophilic DNA ligase from the archaeon Thermococcus fumicolans. FEMS Microbiol. Lett. 2004, 236(2):267-273. 10.1016/j.femsle.2004.05.045.
96. Keppetipola N., Shuman S. Characterization of a thermophilic ATP-dependent DNA ligase from the euryarchaeon Pyrococcus horikoshii. J. Bacteriol. 2005, 187(20):6902-6908. 10.1128/JB.187.20.6902-6908.2005.
97. Jeon S.-J., Ishikawa K. A novel ADP-dependent DNA ligase from Aeropyrum pernix K1. FEBS Lett. 2003, 550(1-3):69-73. 10.1016/S0014-5793(03)00821-4.
98. +-dependent DNA ligases share an essential function in the halophilic archaeon Haloferax volcanii. Mol. Microbiol. 2006, 59(3):743-752. 10.1111/j.1365-2958.2005.04975.x.
99. Kiyonari S. Identification of a novel binding motif in Pyrococcus furiosus DNA ligase for the functional interaction with proliferating cell nuclear antigen. J. Biol. Chem. 2006, 281(38):28023-28032. 10.1074/jbc.M603403200.
100. Lundberg K.S., Shoemaker D.D., Adams M.W., Short J.M., Sorge J.A., Mathur E.J. High-fidelity amplification using a thermostable DNA polymerase isolated from Pyrococcus furiosus. Gene 1991, 108(1):1-6. 10.1016/0378-1119(91)90480-Y.
101. Connolly B.A. Recognition of deaminated bases by archaeal family-B DNA polymerases. Biochem. Soc. Trans. 2009, 37(Pt 1):65-68. 10.1042/BST0370065.
102. Wynne S.A., Pinheiro V.B., Holliger P., Leslie A.G.W. Structures of an Apo and a binary complex of an evolved archeal B family DNA polymerase capable of synthesising highly Cy-Dye labelled DNA. PLoS ONE 2013, 8(8):e70892. Ed. by G. Maga. 10.1371/journal.pone.0070892.
103. Liu X.-P., Liu J.-H. Characterization of family IV UDG from Aeropyrum pernix and its application in Hot-Start PCR by family B DNA polymerase. PLoS ONE 2011, 6(11):e27248. Ed. by S.-Y. Xu. 10.1371/journal.pone.0027248.
104. Evans T.C., Nichols N.M. DNA repair enzymes. Curr. Protoc. Mol. Biol. 2008, (Chapter 3, Unit3.9). 10.1002/0471142727.mb0309s84.
105. Dabrowski S., Brillowska-Dabrowska A., Ahring B.K. Recombinant thermostable AP exonuclease from Thermoanaerobacter tengcongensis: cloning, expression, purification, properties and PCR application. Pol. J. Microbiol. 2013, 62(2):121-129.
106. Wilson R.H., Morton S.K., Deiderick H., Gerth M.L., Paul H.A., Gerber I., Patel A., Ellington A.D., Hunicke-Smith S.P., Patrick W.M. Engineered DNA ligases with improved activities in vitro. Protein Eng. Des. Sel. 2013, 26(7):471-478. 10.1093/protein/gzt024.