DNA replication is essential for all life forms. Although the process is fundamentally conserved in the three domains of life, bioinformatic, biochemical, structural, and genetic studies have demonstrated that the process and the proteins involved in archaeal DNA replication are more similar to those in eukaryal DNA replication than in bacterial DNA replication, but have some archaeal-specific features. The archaeal replication system, however, is not monolithic, and there are some differences in the replication process between different species. In this review, the current knowledge of the mechanisms governing DNA replication in Archaea is summarized. The general features of the replication process as well as some of the differences are discussed.


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Literature Cited

  1. Aravind L, Koonin EV. 1.  1998. Phosphoesterase domains associated with DNA polymerases of diverse origins. Nucleic Acids Res. 26:3746–52 [Google Scholar]
  2. Aravind L, Koonin EV. 2.  1999. DNA-binding proteins and evolution of transcription regulation in the archaea. Nucleic Acids Res. 27:4658–70 [Google Scholar]
  3. Arora J, Goswami K, Saha S. 3.  2014. Characterization of the replication initiator Orc1/Cdc6 from the archaeon Picrophilus torridus. J. Bacteriol. 196:276–86 [Google Scholar]
  4. Balakrishnan L, Bambara RA. 4.  2013. Flap endonuclease 1. Annu. Rev. Biochem. 82:119–38 [Google Scholar]
  5. Balakrishnan L, Bambara RA. 5.  2013. Okazaki fragment metabolism. Cold Spring Harb. Perspect. Biol. 5:a010173 [Google Scholar]
  6. Barry ER, Lovett JE, Costa A, Lea SM, Bell SD. 6.  2009. Intersubunit allosteric communication mediated by a conserved loop in the MCM helicase. Proc. Natl. Acad. Sci. USA 106:1051–56 [Google Scholar]
  7. Barry ER, McGeoch AT, Kelman Z, Bell SD. 7.  2007. Archaeal MCM has separable processivity, substrate choice and helicase domains. Nucleic Acids Res. 35:988–98 [Google Scholar]
  8. Beattie TR, Bell SD. 8.  2012. Coordination of multiple enzyme activities by a single PCNA in archaeal Okazaki fragment maturation. EMBO J. 31:1556–67 [Google Scholar]
  9. Bell SD. 9.  2011. DNA replication: archaeal oriGINS. BMC Biol. 9:36 [Google Scholar]
  10. Bell SD. 10.  2012. Archaeal orc1/cdc6 proteins. Subcell. Biochem. 62:59–69 [Google Scholar]
  11. Bell SD, Botchan MR. 11.  2013. The minichromosome maintenance replicative helicase. Cold Spring Harb. Perspect. Biol. 5:a012807 [Google Scholar]
  12. Bermudez VP, Farina A, Raghavan V, Tappin I, Hurwitz J. 12.  2011. Studies on human DNA polymerase ε and GINS complex and their role in DNA replication. J. Biol. Chem. 286:28963–77 [Google Scholar]
  13. Berquist BR, DasSarma P, DasSarma S. 13.  2007. Essential and non-essential DNA replication genes in the model halophilic Archaeon, Halobacterium sp. NRC-1. BMC Genet. 8:31 [Google Scholar]
  14. Berthon J, Cortez D, Forterre P. 14.  2008. Genomic context analysis in Archaea suggests previously unrecognized links between DNA replication and translation. Genome Biol. 9:R71 [Google Scholar]
  15. Boulikas T. 15.  1996. Common structural features of replication origins in all life forms. J. Cell Biochem. 60:297–316 [Google Scholar]
  16. Brewster AS, Chen XS. 16.  2010. Insights into the MCM functional mechanism: lessons learned from the archaeal MCM complex. Crit. Rev. Biochem. Mol. Biol. 45:243–56 [Google Scholar]
  17. Brewster AS, Slaymaker IM, Afif SA, Chen XS. 17.  2010. Mutational analysis of an archaeal minichromosome maintenance protein exterior hairpin reveals critical residues for helicase activity and DNA binding. BMC Mol. Biol. 11:62 [Google Scholar]
  18. Chapados BR, Hosfield DJ, Han S, Qiu J, Yelent B. 18.  et al. 2004. Structural basis for FEN-1 substrate specificity and PCNA-mediated activation in DNA replication and repair. Cell 116:39–50 [Google Scholar]
  19. Chemnitz Galal W, Pan M, Giulian G, Yuan W, Li S. 19.  et al. 2012. Formation of dAMP-glycerol and dAMP-Tris derivatives by the Thermococcus kodakaraensis DNA primase. J. Biol. Chem. 287:16220–29 [Google Scholar]
  20. Chemnitz Galal W, Pan M, Kelman Z, Hurwitz J. 20.  2012. Characterization of the DNA primase complex isolated from the archaeon, Thermococcus kodakaraensis. J. Biol. Chem. 287:16209–19 [Google Scholar]
  21. Chen SH, Chan N-L, Hsieh T-S. 21.  2013. New mechanistic and functional insights into DNA topoisomerases. Annu. Rev. Biochem. 82:139–70 [Google Scholar]
  22. Chia N, Cann I, Olsen GJ. 22.  2010. Evolution of DNA replication protein complexes in eukaryotes and archaea. PLoS ONE 5:e10866 [Google Scholar]
  23. Chong JP, Hayashi MK, Simon MN, Xu RM, Stillman B. 23.  2000. A double-hexamer archaeal minichromosome maintenance protein is an ATP-dependent DNA helicase. Proc. Natl. Acad. Sci. USA 97:1530–35 [Google Scholar]
  24. Connolly BA. 24.  2009. Recognition of deaminated bases by archaeal family-B DNA polymerases. Biochem. Soc. Trans. 37:65–68 [Google Scholar]
  25. Corn JE, Pease PJ, Hura GL, Berger JM. 25.  2005. Crosstalk between primase subunits can act to regulate primer synthesis in trans. Mol. Cell 20:391–401 [Google Scholar]
  26. Cortez D, Quevillon-Cheruel S, Gribaldo S, Desnoues N, Sezonov G. 26.  et al. 2010. Evidence for a Xer/dif system for chromosome resolution in archaea. PLoS Genet. 6:e1001166 [Google Scholar]
  27. Costa A, Hood IV, Berger JM. 27.  2013. Mechanisms for initiating cellular DNA replication. Annu. Rev. Biochem. 82:25–54 [Google Scholar]
  28. Costa A, Onesti S. 28.  2009. Structural biology of MCM helicases. Crit. Rev. Biochem. Mol. Biol. 44:326–42 [Google Scholar]
  29. Čuboňová L, Richardson T, Burkhart BW, Kelman Z, Reeve JN. 29.  et al. 2013. Archaeal DNA polymerase D but not DNA polymerase B is required for genome replication in Thermococcus kodakarensis. J. Bacteriol. 195:2322–28 [Google Scholar]
  30. De Felice M, Esposito L, Pucci B, De Falco M, Manco G. 30.  et al. 2004. Modular organization of a Cdc6-like protein from the crenarchaeon Sulfolobus solfataricus. Biochem. J. 381:645–53 [Google Scholar]
  31. Desogus G, Onesti S, Brick P, Rossi M, Pisani FM. 31.  1999. Identification and characterization of a DNA primase from the hyperthermophilic archaeon Methanococcus jannaschii. Nucleic Acids Res. 27:4444–50 [Google Scholar]
  32. Dickey TH, Altschuler SE, Wuttke DS. 32.  2013. Single-stranded DNA-binding proteins: multiple domains for multiple functions. Structure 21:1074–84 [Google Scholar]
  33. Dieckman LM, Freudenthal BD, Washington MT. 33.  2012. PCNA structure and function: insights from structures of PCNA complexes and post-translationally modified PCNA. Subcell. Biochem. 62:281–99 [Google Scholar]
  34. Duderstadt KE, Berger JM. 34.  2008. AAA+ ATPases in the initiation of DNA replication. Crit. Rev. Biochem. Mol. Biol. 43:163–87 [Google Scholar]
  35. Duderstadt KE, Berger JM. 35.  2012. A structural framework for replication origin opening by AAA+initiation factors. Curr. Opin. Struct. Biol. 23:144–53 [Google Scholar]
  36. Dueber EL, Corn JE, Bell SD, Berger JM. 36.  2007. Replication origin recognition and deformation by a heterodimeric archaeal Orc1 complex. Science 317:1210–13 [Google Scholar]
  37. Duggin IG, Dubarry N, Bell SD. 37.  2011. Replication termination and chromosome dimer resolution in the archaeon Sulfolobus solfataricus. EMBO J. 30:145–53 [Google Scholar]
  38. Farkas JA, Picking JW, Santangelo TJ. 38.  2013. Genetic techniques for the archaea. Annu. Rev. Genet. 47:539–61 [Google Scholar]
  39. Finger LD, Atack JM, Tsutakawa S, Classen S, Tainer J. 39.  et al. 2012. The wonders of flap endonucleases: structure, function, mechanism and regulation. Subcell. Biochem. 62:301–26 [Google Scholar]
  40. Fletcher RJ, Bishop BE, Leon RP, Sclafani RA, Ogata CM, Chen XS. 40.  2003. The structure and function of MCM from archaeal M. thermoautotrophicum. Nat. Struct. Biol. 10:160–67 [Google Scholar]
  41. Flores-Rozas H, Kelman Z, Dean FB, Pan ZQ, Harper JW. 41.  et al. 1994. Cdk-interacting protein 1 directly binds with proliferating cell nuclear antigen and inhibits DNA replication catalyzed by the DNA polymerase δ holoenzyme. Proc. Natl. Acad. Sci. USA 91:8655–59 [Google Scholar]
  42. Forterre P. 42.  2012. Introduction and historical perspective. DNA Topoisomerases and Cancer Y Pommier 1–52 New York: Humana Press [Google Scholar]
  43. Forterre P, Elie C, Kohiyama M. 43.  1984. Aphidicolin inhibits growth and DNA synthesis in halophilic archaebacteria. J. Bacteriol. 159:800–2 [Google Scholar]
  44. Frick DN, Richardson CC. 44.  2001. DNA primases. Annu. Rev. Biochem. 70:39–80 [Google Scholar]
  45. Gaudier M, Schuwirth BS, Westcott SL, Wigley DB. 45.  2007. Structural basis of DNA replication origin recognition by an ORC protein. Science 317:1213–16 [Google Scholar]
  46. Grabowski B, Kelman Z. 46.  2001. Autophosphorylation of the archaeal Cdc6 homologues is regulated by DNA. J. Bacteriol. 183:5459–64 [Google Scholar]
  47. Grabowski B, Kelman Z. 47.  2003. Archaeal DNA replication: eukaryal proteins in a bacterial context. Annu. Rev. Microbiol. 57:487–516 [Google Scholar]
  48. Greenough L, Menin JF, Desai NS, Kelman Z, Gardner AF. 48.  2014. Characterization of Family D DNA polymerase from Thermococcus sp. 9°N. Extremophiles 18:653–64 [Google Scholar]
  49. Gulbis JM, Kelman Z, Hurwitz J, O'Donnell M, Kuriyan J. 49.  1996. Structure of the C-terminal region of p21WAF1/CIP1 complexed with human PCNA. Cell 87:297–306 [Google Scholar]
  50. Guy L, Saw JH, Ettema TJG. 50.  2014. The archaeal legacy of eukaryotes: a phylogenomic perspective. Cold Spring Harb. Perspect. Biol. In press
  51. Haugland GT, Sakakibara N, Pey AL, Rollor CR, Birkeland N-K, Kelman Z. 51.  2008. Thermoplasma acidophilum Cdc6 protein stimulates MCM helicase activity by regulating its ATPase activity. Nucleic Acids Res 36:5602–9 [Google Scholar]
  52. Haugland GT, Shin J-H, Birkeland NK, Kelman Z. 52.  2006. Stimulation of MCM helicase activity by a Cdc6 protein in the archaeon Thermoplasma acidophilum. Nucleic Acids Res. 34:6337–44 [Google Scholar]
  53. Hawkins M, Malla S, Blythe MJ, Nieduszynski CA, Allers T. 53.  2013. Accelerated growth in the absence of DNA replication origins. Nature 503:544–47 [Google Scholar]
  54. Henneke G. 54.  2012. In vitro reconstitution of RNA primer removal in Archaea reveals the existence of two pathways. Biochem. J. 447:271–80 [Google Scholar]
  55. Henneke G, Flament D, Hubscher U, Querellou J, Raffin JP. 55.  2005. The hyperthermophilic euryarchaeota Pyrococcus abyssi likely requires the two DNA polymerases D and B for DNA replication. J. Mol. Biol. 350:53–64 [Google Scholar]
  56. Henneke G, Koundrioukoff S, Hubscher U. 56.  2003. Phosphorylation of human Fen1 by cyclin-dependent kinase modulates its role in replication fork regulation. Oncogene 22:4301–13 [Google Scholar]
  57. Howes TR, Tomkinson AE. 57.  2012. DNA ligase I, the replicative DNA ligase. Subcell. Biochem. 62:327–41 [Google Scholar]
  58. Indiani C, O'Donnell M. 58.  2006. The replication clamp-loading machine at work in the three domains of life. Nat. Rev. Mol. Cell Biol. 7:751–61 [Google Scholar]
  59. Ishino S, Fujino S, Tomita H, Ogino H, Takao K. 59.  et al. 2011. Biochemical and genetical analyses of the three MCM genes from the hyperthermophilic archaeon, Thermococcus kodakarensis. Genes Cells 16:1176–89 [Google Scholar]
  60. Ishino Y, Ishino S. 60.  2012. Rapid progress of DNA replication studies in Archaea, the third domain of life. Sci. China Life Sci. 55:386–403 [Google Scholar]
  61. Ishino S, Kelman LM, Kelman Z, Ishino Y. 61.  2013. The archaeal DNA replication machinery: past, present and future. Genes Genet. Syst. 88:315–19 [Google Scholar]
  62. Iyer LM, Koonin EV, Leipe DD, Aravind L. 62.  2005. Origin and evolution of the archaeo-eukaryotic primase superfamily and related palm-domain proteins: structural insights and new members. Nucleic Acids Res. 33:3875–96 [Google Scholar]
  63. Jenkinson ER, Chong JP. 63.  2006. Minichromosome maintenance helicase activity is controlled by N- and C-terminal motifs and requires the ATPase domain helix-2 insert. Proc. Natl. Acad. Sci. USA 103:7613–18 [Google Scholar]
  64. Johnson A, O'Donnell M. 64.  2005. Cellular DNA replicases: components and dynamics at the replication fork. Annu. Rev. Biochem. 74:283–315 [Google Scholar]
  65. Kamada K. 65.  2012. The GINS complex: structure and function. Subcell. Biochem. 62:135–56 [Google Scholar]
  66. Kasiviswanathan R, Shin J-H, Kelman Z. 66.  2005. Interactions between the archaeal Cdc6 and MCM proteins modulate their biochemical properties. Nucleic Acids Res. 33:4940–50 [Google Scholar]
  67. Kasiviswanathan R, Shin J-H, Melamud E, Kelman Z. 67.  2004. Biochemical characterization of the Methano-thermobacter thermautotrophicus minichromosome maintenance (MCM) helicase N-terminal domains. J. Biol. Chem. 279:28358–66 [Google Scholar]
  68. Kelch BA, Makino DL, O'Donnell M, Kuriyan J. 68.  2011. How a DNA polymerase clamp loader opens a sliding clamp. Science 334:1675–80 [Google Scholar]
  69. Kelch BA, Makino DL, O'Donnell M, Kuriyan J. 69.  2012. Clamp loader ATPases and the evolution of DNA replication machinery. BMC Biol. 10:34 [Google Scholar]
  70. Kelly TJ, Simancek P, Brush GS. 70.  1998. Identification and characterization of a single-stranded DNA-binding protein from the archaeon Methanococcus jannaschii. Proc. Natl. Acad. Sci. USA 95:14634–39 [Google Scholar]
  71. Kelman LM, Kelman Z. 71.  2003. Archaea: an archetype for replication initiation studies?. Mol. Microbiol. 48:605–15 [Google Scholar]
  72. Kelman LM, Kelman Z. 72.  2004. Multiple origins of replication in archaea. Trends Microbiol. 12:399–401 [Google Scholar]
  73. Kelman Z. 73.  2000. DNA replication in the third domain (of life). Curr. Protein Pept. Sci. 1:139–54 [Google Scholar]
  74. Kelman Z. 74.  2000. The replication origin of archaea is finally revealed. Trends Biochem. Sci. 25:521–23 [Google Scholar]
  75. Kelman Z, Finkelstein J, O'Donnell M. 75.  1995. Why have six-fold symmetry?. Curr. Biol. 5:1239–42 [Google Scholar]
  76. Kelman Z, Hurwitz J. 76.  1998. Protein-PCNA interactions: a DNA-scanning mechanism?. Trends Biochem. Sci. 23:236–38 [Google Scholar]
  77. Kelman Z, Hurwitz J. 77.  2000. A unique organization of the protein subunits of the DNA polymerase clamp loader in the archaeon Methanobacterium thermoautotrophicum ΔH. J. Biol. Chem. 275:7327–36 [Google Scholar]
  78. Kelman Z, Hurwitz J. 78.  2003. Structural lessons in DNA replication from the third domain of life. Nat. Struct. Biol. 10:148–50 [Google Scholar]
  79. Kelman Z, Lee JK, Hurwitz J. 79.  1999. The single minichromosome maintenance protein of Methanobacterium thermoautotrophicum ΔH contains DNA helicase activity. Proc. Natl. Acad. Sci. USA 96:14783–88 [Google Scholar]
  80. Kelman Z, O'Donnell M. 80.  1995. Structural and functional similarities of prokaryotic and eukaryotic DNA polymerase sliding clamps. Nucleic Acids Res. 23:3613–20 [Google Scholar]
  81. Kelman Z, Pietrokovski S, Hurwitz J. 81.  1999. Isolation and characterization of a split B-type DNA polymerase from the archaeon Methanobacterium thermoautotrophicum ΔH. J. Biol. Chem. 274:28751–61 [Google Scholar]
  82. Kelman Z, Yuzhakov A, Andjelkovic J, O'Donnell M. 82.  1998. Devoted to the lagging strand: the χ subunit of DNA polymerase III holoenzyme contacts SSB to promote processive elongation and sliding clamp assembly. EMBO J. 17:2436–49 [Google Scholar]
  83. Kennelly PJ. 83.  2003. Archaeal protein kinases and protein phosphatases: insights from genomics and biochemistry. Biochem. J. 370:373–89 [Google Scholar]
  84. Kerr ID, Wadsworth RI, Cubeddu L, Blankenfeldt W, Naismith JH, White MF. 84.  2003. Insights into ssDNA recognition by the OB fold from a structural and thermodynamic study of Sulfolobus SSB protein. EMBO J. 22:2561–70 [Google Scholar]
  85. Kesti T, Flick K, Keranen S, Syvaoja JE, Wittenberg C. 85.  1999. DNA polymerase ε catalytic domains are dispensable for DNA replication, DNA repair, and cell viability. Mol. Cell 3:679–85 [Google Scholar]
  86. Kletzin A. 86.  1992. Molecular characterisation of a DNA ligase gene of the extremely thermophilic archaeon Desulfurolobus ambivalens shows close phylogenetic relationship to eukaryotic ligases. Nucleic Acids Res. 20:5389–96 [Google Scholar]
  87. Klinge S, Hirst J, Maman JD, Krude T, Pellegrini L. 87.  2007. An iron-sulfur domain of the eukaryotic primase is essential for RNA primer synthesis. Nat. Struct. Mol. Biol. 14:875–77 [Google Scholar]
  88. Komori K, Ishino Y. 88.  2001. Replication protein A in Pyrococcus furiosus is involved in homologous DNA recombination. J. Biol. Chem. 276:25654–60 [Google Scholar]
  89. Kornberg A, Baker TA. 89.  1992. DNA Replication New York: W.H. Freeman931
  90. Krastanova I, Sannino V, Amenitsch H, Gileadi O, Pisani FM, Onesti S. 90.  2012. Structural and functional insights into the DNA replication factor Cdc45 reveal an evolutionary relationship to the DHH family of phosphoesterases. J. Biol. Chem. 287:4121–28 [Google Scholar]
  91. Krueger S, Shin J-H, Curtis JE, Rubinson KA, Kelman Z. 91.  2014. The solution structure of full-length dodecameric MCM by SANS and molecular modeling. Proteins. In press
  92. Krueger S, Shin J-H, Raghunandan S, Curtis JE, Kelman Z. 92.  2011. Atomistic ensemble modeling and small-angle neutron scattering of intrinsically disordered protein complexes: applied to minichromosome maintenance protein. Biophys. J. 101:2999–3007 [Google Scholar]
  93. Krupovic M, Gribaldo S, Bamford DH, Forterre P. 93.  2010. The evolutionary history of archaeal MCM helicases: a case study of vertical evolution combined with hitch-hiking of mobile genetic elements. Mol. Biol. Evol. 27:2716–32 [Google Scholar]
  94. Langston LD, Indiani C, O'Donnell M. 94.  2009. Whither the replisome: emerging perspectives on the dynamic nature of the DNA replication machinery. Cell Cycle 8:2686–91 [Google Scholar]
  95. Lao-Sirieix SH, Nookala RK, Roversi P, Bell SD, Pellegrini L. 95.  2005. Structure of the heterodimeric core primase. Nat. Struct. Mol. Biol. 12:1137–44 [Google Scholar]
  96. Lao-Sirieix SH, Pellegrini L, Bell SD. 96.  2005. The promiscuous primase. Trends Genet. 21:568–72 [Google Scholar]
  97. Lee C, Hong B, Choi JM, Kim Y, Watanabe S. 97.  et al. 2004. Structural basis for inhibition of the replication licensing factor Cdt1 by geminin. Nature 430:913–17 [Google Scholar]
  98. Leonard AC, Grimwade JE. 98.  2011. Regulation of DnaA assembly and activity: taking directions from the genome. Annu. Rev. Microbiol. 65:19–35 [Google Scholar]
  99. Li Z, Huang RY, Yopp DC, Hileman TH, Santangelo TJ. 99.  et al. 2014. A novel mechanism for regulating the activity of proliferating cell nuclear antigen by a small protein. Nucleic Acids Res. 42:5776–89 [Google Scholar]
  100. Li Z, Kelman LM, Kelman Z. 100.  2013. Thermococcus kodakarensis DNA replication. Biochem. Soc. Trans. 41:332–38 [Google Scholar]
  101. Li Z, Pan M, Santangelo TJ, Chemnitz W, Yuan W. 101.  et al. 2011. A novel DNA nuclease is stimulated by association with the GINS complex. Nucleic Acids Res. 39:6114–23 [Google Scholar]
  102. Li Z, Santangelo TJ, Čuboňová L, Reeve JN, Kelman Z. 102.  2010. Affinity purification of an archaeal DNA replication protein network. MBio 1:e00221–10 [Google Scholar]
  103. Lindas AC, Bernander R. 103.  2013. The cell cycle of archaea. Nat. Rev. Microbiol. 11:627–38 [Google Scholar]
  104. Liu W, Pucci B, Rossi M, Pisani FM, Ladenstein R. 104.  2008. Structural analysis of the Sulfolobus solfataricus MCM protein N-terminal domain. Nucleic Acids Res. 36:3235–43 [Google Scholar]
  105. Lopez P, Philippe H, Myllykallio H, Forterre P. 105.  1999. Identification of putative chromosomal origins of replication in Archaea. Mol. Microbiol. 32:883–86 [Google Scholar]
  106. Lundgren M, Andersson A, Chen L, Nilsson P, Bernander R. 106.  2004. Three replication origins in Sulfolobus species: synchronous initiation of chromosome replication and asynchronous termination. Proc. Natl. Acad. Sci. USA 101:7046–51 [Google Scholar]
  107. Lundgren M, Bernander R. 107.  2007. Genome-wide transcription map of an archaeal cell cycle. Proc. Natl. Acad. Sci. USA 104:2939–44 [Google Scholar]
  108. MacNeill SA. 108.  2010. Structure and function of the GINS complex, a key component of the eukaryotic replisome. Biochem. J. 425:489–500 [Google Scholar]
  109. MacNeill SA. 109.  2011. Protein-protein interactions in the archaeal core replisome. Biochem. Soc. Trans. 39:163–68 [Google Scholar]
  110. Makarova KS, Koonin EV. 110.  2013. Archaeology of eukaryotic DNA replication. Cold Spring Harb. Perspect. Biol. 5a012963
  111. Makarova KS, Koonin EV, Kelman Z. 111.  2012. The CMG (CDC45/RecJ, MCM, GINS) complex is a conserved component of the DNA replication system in all archaea and eukaryotes. Biol. Direct 7:7 [Google Scholar]
  112. Makarova KS, Wolf YI, Mekhedov SL, Mirkin BG, Koonin EV. 112.  2005. Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell. Nucleic Acids Res. 33:4626–38 [Google Scholar]
  113. Makarova KS, Yutin N, Bell SD, Koonin EV. 113.  2010. Evolution of diverse cell division and vesicle formation systems in Archaea. Nat. Rev. Microbiol. 8:731–41 [Google Scholar]
  114. Marinsek N, Barry ER, Makarova KS, Dionne I, Koonin EV, Bell SD. 114.  2006. GINS, a central nexus in the archaeal DNA replication fork. EMBO Rep. 7:539–45 [Google Scholar]
  115. Masai H, Matsumoto S, You Z, Yoshizawa-Sugata N, Oda M. 115.  2010. Eukaryotic chromosome DNA replication: where, when, and how?. Annu. Rev. Biochem. 79:89–130 [Google Scholar]
  116. Matsui E, Nishio M, Yokoyama H, Harata K, Darnis S, Matsui I. 116.  2003. Distinct domain functions regulating de novo DNA synthesis of thermostable DNA primase from hyperthermophile Pyrococcus horikoshii. Biochemistry 42:14968–76 [Google Scholar]
  117. Matsui I, Urushibata Y, Shen Y, Matsui E, Yokoyama H. 117.  2011. Novel structure of an N-terminal domain that is crucial for the dimeric assembly and DNA-binding of an archaeal DNA polymerase D large subunit from Pyrococcus horikoshii. FEBS Lett. 585:452–58 [Google Scholar]
  118. Matsunaga F, Forterre P, Ishino Y, Myllykallio H. 118.  2001. In vivo interactions of archaeal Cdc6/Orc1 and minichromosome maintenance protein with the replication origin. Proc. Natl. Acad. Sci. USA 98:11152–57 [Google Scholar]
  119. Matsunaga F, Norais C, Forterre P, Myllykallio H. 119.  2003. Identification of short “eukaryotic” Okazaki fragments synthesized from a prokaryotic replication origin. EMBO Rep. 4:154–58 [Google Scholar]
  120. Maupin-Furlow JA. 120.  2013. Ubiquitin-like proteins and their roles in archaea. Trends Microbiol. 21:31–38 [Google Scholar]
  121. Mayanagi K, Kiyonari S, Saito M, Shirai T, Ishino Y, Morikawa K. 121.  2009. Mechanism of replication machinery assembly as revealed by the DNA ligase-PCNA-DNA complex architecture. Proc. Natl. Acad. Sci. USA 106:4647–52 [Google Scholar]
  122. McGeoch AT, Trakselis MA, Laskey RA, Bell SD. 122.  2005. Organization of the archaeal MCM complex on DNA and implications for the helicase mechanism. Nat. Struct. Mol. Biol. 12:756–62 [Google Scholar]
  123. Medagli B, Onesti S. 123.  2013. Structure and mechanism of hexameric helicases. Adv. Exp. Med. Biol. 767:75–95 [Google Scholar]
  124. Miyata T, Oyama T, Mayanagi K, Ishino S, Ishino Y, Morikawa K. 124.  2004. The clamp-loading complex for processive DNA replication. Nat. Struct. Mol. Biol. 11:632–36 [Google Scholar]
  125. Morgunova E, Gray FC, MacNeill SA, Ladenstein R. 125.  2009. Structural insights into the adaptation of proliferating cell nuclear antigen (PCNA) from Haloferax volcanii to a high-salt environment. Acta Crystallogr. D 65:1081–88 [Google Scholar]
  126. Myllykallio H, Lopez P, Lopez-Garcia P, Heilig R, Saurin W. 126.  et al. 2000. Bacterial mode of replication with eukaryotic-like machinery in a hyperthermophilic archaeon. Science 288:2212–15 [Google Scholar]
  127. O'Donnell M, Langston L, Stillman B. 127.  2013. Principles and concepts of DNA replication in bacteria, archaea, and eukarya. Cold Spring Harb. Perspect. Biol. 5:a010108 [Google Scholar]
  128. Ogino H, Ishino S, Mayanagi K, Haugland GT, Birkeland NK. 128.  et al. 2011. The GINS complex from the thermophilic archaeon, Thermoplasma acidophilum may function as a homotetramer in DNA replication. Extremophiles 15:529–39 [Google Scholar]
  129. Onesti S, MacNeill SA. 129.  2013. Structure and evolutionary origins of the CMG complex. Chromosoma 122:47–53 [Google Scholar]
  130. Oyama T, Ishino S, Fujino S, Ogino H, Shirai T. 130.  et al. 2011. Architectures of archaeal GINS complexes, essential DNA replication initiation factors. BMC Biol. 9:28 [Google Scholar]
  131. Pan M, Kelman LM, Kelman Z. 131.  2011. The archaeal PCNA proteins. Biochem. Soc. Trans. 39:20–24 [Google Scholar]
  132. Pan M, Santangelo TJ, Čuboňová L, Li Z, Metangmo H. 132.  et al. 2013. Thermococcus kodakarensis has two functional PCNA homologues but only one is required for viability. Extremophiles 17:453–61 [Google Scholar]
  133. Pan M, Santangelo TJ, Li Z, Reeve JN, Kelman Z. 133.  2011. Thermococcus kodakarensis encodes three MCM homologs but only one is essential. Nucleic Acids Res. 39:9671–80 [Google Scholar]
  134. Pascal JM, O'Brien PJ, Tomkinson AE, Ellenberger T. 134.  2004. Human DNA ligase I completely encircles and partially unwinds nicked DNA. Nature 432:473–78 [Google Scholar]
  135. Pascal JM, Tsodikov OV, Hura GL, Song W, Cotner EA. 135.  et al. 2006. A flexible interface between DNA ligase and PCNA supports conformational switching and efficient ligation of DNA. Mol. Cell 24:279–91 [Google Scholar]
  136. Paytubi S, McMahon SA, Graham S, Liu H, Botting CH. 136.  et al. 2012. Displacement of the canonical single-stranded DNA-binding protein in the Thermoproteales. Proc. Natl. Acad. Sci. USA 109:E398–405 [Google Scholar]
  137. Pellegrini L. 137.  2012. The Pol α-primase complex. Subcell. Biochem. 62:157–69 [Google Scholar]
  138. Pelve EA, Lindas AC, Knoppel A, Mira A, Bernander R. 138.  2012. Four chromosome replication origins in the archaeon Pyrobaculum calidifontis. Mol. Microbiol. 85:986–95 [Google Scholar]
  139. Perler FB, Kumar S, Kong H. 139.  1996. Thermostable DNA polymerases. Adv. Protein Chem. 48:377–435 [Google Scholar]
  140. Pluchon PF, Fouqueau T, Creze C, Laurent S, Briffotaux J. 140.  et al. 2013. An extended network of genomic maintenance in the archaeon Pyrococcus abyssi highlights unexpected associations between eucaryotic homologs. PLoS ONE 8:e79707 [Google Scholar]
  141. Poplawski A, Grabowski B, Long SE, Kelman Z. 141.  2001. The zinc finger domain of the archaeal minichromosome maintenance protein is required for helicase activity. J. Biol. Chem. 276:49371–77 [Google Scholar]
  142. Prakash A, Borgstahl GE. 142.  2012. The structure and function of replication protein A in DNA replication. Subcell. Biochem. 62:171–96 [Google Scholar]
  143. Raymann K, Forterre P, Brochier-Armanet C, Gribaldo S. 143.  2014. Global phylogenomic analysis disentangles the complex evolutionary history of DNA replication in Archaea. Genome Biol. Evol. 6:192–212 [Google Scholar]
  144. Reimann J, Esser D, Orell A, Amman F, Pham TK. 144.  et al. 2013. Archaeal signal transduction: impact of protein phosphatase deletions on cell size, motility and energy metabolism in Sulfolobus acidocaldarius. Mol. Cell. Proteomics 12:3908–23 [Google Scholar]
  145. Remus D, Beuron F, Tolun G, Griffith JD, Morris EP, Diffley JF. 145.  2009. Concerted loading of Mcm2-7 double hexamers around DNA during DNA replication origin licensing. Cell 139:719–30 [Google Scholar]
  146. Reyes-Lamothe R, Nicolas E, Sherratt DJ. 146.  2012. Chromosome replication and segregation in bacteria. Annu. Rev. Genet. 46:121–43 [Google Scholar]
  147. Robbins JB, McKinney MC, Guzman CE, Sriratana B, Fitz-Gibbon S. 147.  et al. 2005. The euryarchaeota, nature's medium for engineering of single-stranded DNA-binding proteins. J. Biol. Chem. 280:15325–39 [Google Scholar]
  148. Robinson NP, Bell SD. 148.  2007. Extrachromosomal element capture and the evolution of multiple replication origins in archaeal chromosomes. Proc. Natl. Acad. Sci. USA 104:5806–11 [Google Scholar]
  149. Robinson NP, Dionne I, Lundgren M, Marsh VL, Bernander R, Bell SD. 149.  2004. Identification of two origins of replication in the single chromosome of the archaeon Sulfolobus solfataricus. Cell 116:25–38 [Google Scholar]
  150. Sakakibara N, Kasiviswanathan R, Melamud E, Han M, Schwarz FP, Kelman Z. 150.  2008. Coupling of DNA binding and helicase activity is mediated by a conserved loop in the MCM protein. Nucleic Acids Res. 36:1309–20 [Google Scholar]
  151. Sakakibara N, Kelman LM, Kelman Z. 151.  2009. How is the archaeal MCM helicase assembled at the origin? Possible mechanisms. Biochem. Soc. Trans. 37:7–11 [Google Scholar]
  152. Sakakibara N, Kelman LM, Kelman Z. 152.  2009. Unwinding the structure and function of the archaeal MCM helicase. Mol. Microbiol. 72:286–96 [Google Scholar]
  153. Samson RY, Bell SD. 153.  2011. Cell cycles and cell division in the archaea. Curr. Opin. Microbiol. 14:350–56 [Google Scholar]
  154. Samson RY, Xu Y, Gadelha C, Stone TA, Faqiri JN. 154.  et al. 2013. Specificity and function of archaeal DNA replication initiator proteins. Cell Rep. 3:485–96 [Google Scholar]
  155. Sarmiento F, Mrazek J, Whitman WB. 155.  2013. Genome-scale analysis of gene function in the hydrogenotrophic methanogenic archaeon Methanococcus maripaludis. Proc. Natl. Acad. Sci. USA 110:4726–31 [Google Scholar]
  156. Shechter DF, Ying CY, Gautier J. 156.  2000. The intrinsic DNA helicase activity of Methanobacterium thermoautotrophicum ΔH minichromosome maintenance protein. J. Biol. Chem. 275:15049–59 [Google Scholar]
  157. Shen Y, Tang XF, Matsui E, Matsui I. 157.  2004. Subunit interaction and regulation of activity through terminal domains of the family D DNA polymerase from Pyrococcus horikoshii. Biochem. Soc. Trans. 32:245–49 [Google Scholar]
  158. Shin J-H, Grabowski B, Kasiviswanathan R, Bell SD, Kelman Z. 158.  2003. Regulation of minichromosome maintenance helicase activity by Cdc6. J. Biol. Chem. 278:38059–67 [Google Scholar]
  159. Shin J-H, Heo GY, Kelman Z. 159.  2008. The Methanothermobacter thermautotrophicus Cdc6-2 protein, the putative helicase loader, dissociates the minichromosome maintenance helicase. J. Bacteriol. 190:4091–94 [Google Scholar]
  160. Shin J-H, Heo G-Y, Kelman Z. 160.  2009. The Methanothermobacter thermautotrophicus MCM helicase is active as a hexameric ring. J. Biol. Chem. 284:540–46 [Google Scholar]
  161. Shin J-H, Kelman Z. 161.  2006. The replicative helicases of bacteria, archaea and eukarya can unwind RNA-DNA hybrid substrates. J. Biol. Chem. 281:26914–21 [Google Scholar]
  162. Shin J-H, Santangelo TJ, Xie Y, Reeve JN, Kelman Z. 162.  2007. Archaeal minichromosome maintenance (MCM) helicase can unwind DNA bound by archaeal histones and transcription factors. J. Biol. Chem. 282:4908–15 [Google Scholar]
  163. Skowyra A, MacNeill SA. 163.  2012. Identification of essential and non-essential single-stranded DNA-binding proteins in a model archaeal organism. Nucleic Acids Res. 40:1077–90 [Google Scholar]
  164. Slaymaker IM, Chen XS. 164.  2012. MCM structure and mechanics: what we have learned from archaeal MCM. Subcell. Biochem. 62:89–111 [Google Scholar]
  165. Sriskanda V, Kelman Z, Hurwitz J, Shuman S. 165.  2000. Characterization of an ATP-dependent DNA ligase from the thermophilic archaeon Methanobacterium thermoautotrophicum. Nucleic Acids Res. 28:2221–28 [Google Scholar]
  166. Stelter M, Gutsche I, Kapp U, Bazin A, Bajic G. 166.  et al. 2012. Architecture of a dodecameric bacterial replicative helicase. Structure 20:554–64 [Google Scholar]
  167. Swiatek A, MacNeill SA. 167.  2010. The archaeo-eukaryotic GINS proteins and the archaeal primase catalytic subunit PriS share a common domain. Biol. Direct 5:17 [Google Scholar]
  168. Takahashi TS, Wigley DB, Walter JC. 168.  2005. Pumps, paradoxes and ploughshares: mechanism of the MCM2-7 DNA helicase. Trends Biochem. Sci. 30:437–44 [Google Scholar]
  169. Uemori T, Sato Y, Kato I, Doi H, Ishino Y. 169.  1997. A novel DNA polymerase in the hyperthermophilic archaeon, Pyrococcus furiosus: gene cloning, expression, and characterization. Genes Cells 2:499–512 [Google Scholar]
  170. Vivona JB, Kelman Z. 170.  2003. The diverse spectrum of sliding clamp interacting proteins. FEBS Lett. 546:167–72 [Google Scholar]
  171. Wadsworth RI, White MF. 171.  2001. Identification and properties of the crenarchaeal single-stranded DNA binding protein from Sulfolobus solfataricus. Nucleic Acids Res. 29:914–20 [Google Scholar]
  172. Wahle E, Lasken RS, Kornberg A. 172.  1989. The dnaB-dnaC replication protein complex of Escherichia coli. II. Role of the complex in mobilizing dnaB functions. J. Biol. Chem. 264:2469–75 [Google Scholar]
  173. Warbrick E, Heatherington W, Lane DP, Glover DM. 173.  1998. PCNA binding proteins in Drosophila melanogaster: the analysis of a conserved PCNA binding domain. Nucleic Acids Res. 26:3925–32 [Google Scholar]
  174. Wigley DB. 174.  2009. ORC proteins: marking the start. Curr. Opin. Struct. Biol. 19:72–78 [Google Scholar]
  175. Williams GJ, Johnson K, Rudolf J, McMahon SA, Carter L. 175.  et al. 2006. Structure of the heterotrimeric PCNA from Sulfolobus solfataricus. Acta Crystallogr. Sect. F 62:944–48 [Google Scholar]
  176. Winter JA, Christofi P, Morroll S, Bunting KA. 176.  2009. The crystal structure of Haloferax volcanii proliferating cell nuclear antigen reveals unique surface charge characteristics due to halophilic adaptation. BMC Struct. Biol. 9:55 [Google Scholar]
  177. Woese CR, Fox GE. 177.  1977. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc. Natl. Acad. Sci. USA 74:5088–90 [Google Scholar]
  178. Wu K, Lai X, Guo X, Hu J, Xiang X, Huang L. 178.  2007. Interplay between primase and replication factor C in the hyperthermophilic archaeon Sulfolobus solfataricus. Mol. Microbiol. 63:826–37 [Google Scholar]
  179. Yamasaki K, Urushibata Y, Yamasaki T, Arisaka F, Matsui I. 179.  2010. Solution structure of the N-terminal domain of the archaeal D-family DNA polymerase small subunit reveals evolutionary relationship to eukaryotic B-family polymerases. FEBS Lett. 584:3370–75 [Google Scholar]
  180. Yao N, Turner J, Kelman Z, Stukenberg PT, Dean F. 180.  et al. 1996. Clamp loading, unloading and intrinsic stability of the PCNA, β and gp45 sliding clamps of human, E. coli and T4 replicases. Genes Cells 1:101–13 [Google Scholar]
  181. Yao NY, O'Donnell M. 181.  2012. The RFC clamp loader: structure and function. Subcell. Biochem. 62:259–79 [Google Scholar]
  182. Yuzhakov A, Kelman Z, Hurwitz J, O'Donnell M. 182.  1999. Multiple competition reactions for RPA order the assembly of the DNA polymerase δ holoenzyme. EMBO J. 18:6189–99 [Google Scholar]
  183. Yuzhakov A, Kelman Z, O'Donnell M. 183.  1999. Trading places on DNA: a three-point switch underlies primer handoff from primase to the replicative DNA polymerase. Cell 96:153–63 [Google Scholar]
  184. Zhang R, Zhang CT. 184.  2003. Multiple replication origins of the archaeon Halobacterium species NRC-1. Biochem. Biophys. Res. Commun. 302:728–34 [Google Scholar]
  185. Zhao A, Gray FC, MacNeill SA. 185.  2006. ATP- and NAD+-dependent DNA ligases share an essential function in the halophilic archaeon Haloferax volcanii. Mol. Microbiol. 59:743–52 [Google Scholar]

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