Origins of DNA replication in the three domains of life

FEBS Journal

Volumn 272, Issue 15, 2005, Pages 3757-3766

  Robinson, Nicholas P ^a   Bell, Stephen D ^a  

^a HUTCHISON MRC RESEARCH CENTRE   (United Kingdom)

Author keywords

Cdc6; DNA Replication; DnaA; MCM; ORC

Indexed keywords

BACTERIAL DNA; CELL CYCLE PROTEIN 6; DNA A;

ARCHAEBACTERIUM; AT RICH SEQUENCE; DNA BINDING; DNA REPLICATION; DNA REPLICATION ORIGIN; DNA STRUCTURE; DNA SYNTHESIS; DROSOPHILA MELANOGASTER; ESCHERICHIA COLI; EUKARYOTE; GENETIC VARIABILITY; GENOME; HALOBACTERIUM; IMMUNOPRECIPITATION; MOLECULAR EVOLUTION; NONHUMAN; PRIORITY JOURNAL; PYROCOCCUS HORIKOSHII; REVIEW; SACCHAROMYCES CEREVISIAE; XENOPUS; YEAST;

ARCHAEA; BACTERIA; DNA REPLICATION; EUKARYOTIC CELLS; EVOLUTION, MOLECULAR; REPLICATION ORIGIN; SACCHAROMYCES CEREVISIAE; SCHIZOSACCHAROMYCES;

BACTERIA (MICROORGANISMS); CELLULAR ORGANISMS; EUKARYOTA;

EID: 23644448872     PISSN: 1742464X     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1742-4658.2005.04768.x     Document Type: Review

References (64)

1. Jacob F, Brenner S & Kuzin F (1963) On the regulation of DNA replication in bacteria. Cold Spring Harbor Symposium. Quant Biol 28, 329-348.
2. Kornberg A & Baker TA (1992) DNA Replication, 2nd edn. Freeman, New York.
3. Fuller RS, Funnell BE & Kornberg A (1984) The dnaA Protein Complex with the E. coli Chromosomal Replication Origin (Oric) and Other DNA Sites. Cell 38, 889-900.
4. Messer W (2002) The bacterial replication initiator DnaA. DnaA and oriC, the bacterial mode to initiate DNA replication. FEMS Micro Rev 26, 355-374.
5. Schaper S & Messer W (1995) Interaction of the initiator protein DnaA of Escherichia coli with its DNA target. J Biol Chem 270, 17622-17626.
6. Speck C & Messer W (2001) Mechanism of origin unwinding: sequential binding of DnaA to double- and single-stranded DNA. EMBO J 20, 1469-1476.
7. Davey MJ, Jeruzalmi D, Kuriyan J & O'Donnell M (2002) Motors and switches: AAA + machines within the replisome. Nat Rev Mol Cell Biol 3, 826-835.
8. Speck C, Weigel C & Messer W (1999) ATP- and ADP-DnaA protein, a molecular switch in gene regulation. EMBO J 18, 6169-6176.
9. Hwang DS & Kornberg A (1992) Opening of the replication origin of Escherichia coli by DnaA protein with protein Hu or Ihf. J Biol Chem 267, 23083-23086.
10. Bramhill D & Kornberg A (1988) A model for initiation at origins of DNA replication. Cell 54, 915-918.
11. Funnell BE, Baker TA & Kornberg A (1987) In vitro assembly of a prepriming complex at the origin of the Escherichia coli chromosome. J Biol Chem 262, 10327-10334.
12. Baker TA, Funnell BE & Kornberg A (1987) Helicase action of DnaB protein during replication from the Escherichia coli chromosomal origin in vitro. J Biol Chem 262, 6877-6885.
13. Fang LH, Davey MJ & O'Donnell M (1999) Replisome assembly at oriC, the replication origin of E. coli, reveals an explanation for initiation sites outside an origin. Mol Cell 4, 541-553.
14. Davey MJ, Fang LH, McInerney P, Georgescu RE & O'Donnell M (2002) The DnaC helicase loader is a dual ATP/ADP switch protein. EMBO J 21, 3148-3159.
15. Schwob E (2004) Flexibility and governance in eukaryotic DNA replication. Curr Opin Microbiol 7, 680-690.
16. Antequera F (2004) Genomic specification and epigenetic regulation of eukaryotic DNA replication origins. EMBO J 23, 4365-4370.
17. Gilbert DM (2004) In search of the holy replicator. Nat Rev Mol Cell Biol 5, 848-855.
18. Aladjem MI & Fanning E (2004) The replicon revisited: an old model learns new tricks in metazoan chromosomes. EMBO Report 5, 686-691.
19. Mechali M (2001) DNA replication origins: from sequence specificity to epigenetics. Nat Rev Genet 2, 640-645.
20. Bell SP & Dutta A (2002) DNA replication in eukaryotic cells. Annu Rev Biochem 71, 333-374.
21. Bell SP (2002) The origin recognition complex: from simple origins to complex functions. Genes Dev 16, 659-672.
22. Bell SP & Stillman B (1992) ATP-dependent recognition of eukaryotic origins of DNA replication by a multiprotein complex. Nature 357, 128-134.
23. Stillman B (2005) Origin recognition and the chromosome cycle. FEBS Lett 579, 877-884.
24. Diffley JF (2004) Regulation of early events in chromosome replication. Curr Biol 14, R778-R786.
25. Mendez J & Stillman B (2003) Perpetuating the double helix: molecular machines at eukaryotic DNA replication origins. Bioessays 25, 1158-1167.
26. Bowers JL, Randell JCW, Chen SY & Bell SP (2004) ATP hydrolysis by ORC catalyzes reiterative Mcm2-7 assembly at a defined origin of replication. Mol Cell 16, 967-978.
27. Geraghty DS, Ding M, Heintz NH & Pederson DS (2000) Premature structural changes at replication origins in a yeast minichromosome maintenance (MCM) mutant. J Biol Chem 275, 18011-18021.
28. Laskey RA & Madine MA (2003) A rotary pumping model for helicase function of MCM proteins at a distance from replication forks. EMBO Report 4, 26-30.
29. Lipford JR & Bell SP (2001) Nucleosomes Positioned by ORC Facilitate the Initiation of DNA Replication. Mol Cell 7, 21-30.
30. Vogelauer M, Rubbi L, Lucas I, Brewer BJ & Grunstein M (2002) Histone Acetylation Regulates the Time of Replication Origin Firing. Mol Cell 10, 1223-1233.
31. Theis JF, Yang C, Schaefer CB & Newlon CS (1999) DNA sequence and functional analysis of homologous ARS elements of Saccharomyces cerevisiae and S. carlsbergensis. Genetics 152, 943-952.
32. Theis JF & Newlon CS (2001) Two compound replication origins in Saccharomyces cerevisiae contain redundant origin recognition complex binding sites. Mol Cell Biol 21, 2790-2801.
33. Wyrick JJ, Aparicio JG, Chen T, Barnett JD, Jennings EG, Young RA, Bell SP & Aparicio OM (2001) Genome-wide distribution of ORC and MCM proteins in S. cerevisiae: High-resolution mapping of replication origins. Science 294, 2357-2360.
34. Raghuraman MK, Winzeler EA, Collingwood D, Hunt S, Wodicka L, Conway A, Lockhart DJ, Davis RW, Brewer BJ & Fangman WL (2001) Replication dynamics of the yeast genome. Science 294, 115-121.
35. Chuang RY & Kelly TJ (1999) The fission yeast homologue of Orc4p binds to replication origin DNA via multiple AT-hooks. Proc Natl Acad Sci USA 96, 2656-2661.
36. Lee JK, Moon KY, Jiang Y & Hurwitz J (2001) The Schizosaccharomyces pombe origin recognition complex interacts with multiple AT-rich regions of the replication origin DNA by means of the AT-hook domains of the spOrc4 protein. Proc Natl Acad Sci USA 98, 13589-13594.
37. Kong D & DePamphilis ML (2001) Site-specific DNA binding of the Schizosaccharomyces pombe origin recognition complex is determined by the Orc4 subunit. Mol Cell Biol 21, 8095-8103.
38. Segurado M, de Luis A & Antequera F (2003) Genome-wide distribution of DNA replication origins at A + T-rich islands in Schizosaccharomyces pombe. EMBO Rep 4, 1048-1053.
39. Dai JL, Chuang RY & Kelly TJ (2005) DNA replication origins in the Schizosaccharomyces pombe genome. Proc Natl Acad Sci USA 102, 337-342.
40. Coverley D & Laskey RA (1994) Regulation of eukaryotic DNA replication. Annu Rev Biochem 63, 745-776.
41. Austin RJ, Orr-Weaver TL & Bell SP (1999) Drosophila ORC specifically binds to ACE3, an origin of DNA replication control element. Genes Dev 13, 2639-2649.
42. Beall EL, Manak JR, Zhou S, Bell M, Lipsick JS & Botchan MR (2002) Role for a Drosophila Myb-containing protein complex in site-specific DNA replication. Nature 420, 833-837.
43. Aggarwal BD & Calvi BR (2004) Chromatin regulates origin activity in Drosophila follicle cells. Nature 430, 372-376.
44. MacAlpine DM, Rodriguez HK & Bell SP (2004) Coordination of replication and transcription along a Drosophila chromosome. Genes Dev 18, 3094-3105.
45. Danis E, Brodolin K, Menut S, Maiorano D, Girard-Reydet C & Mechali M (2004) Specification of a DNA replication origin by a transcription complex. Nat Cell Biol 6, 721-730.
46. Stehle IM, Scinteie MF, Baiker A, Jenke ACW & Lipps HJ (2003) Exploiting a minimal system to study the epigenetic control of DNA replication: the interplay between transcription and replication. Chromosome Res 11, 413-421.
47. Schaarschmidt D, Baltin J, Stehle IM, Lipps HJ & Knippers R (2004) An episomal mammalian replicon: sequence-independent binding of the origin recognition complex. EMBO J 23, 191-201.
48. Remus D, Beall EL & Botchan MR (2004) DNA topology, not DNA sequence, is a critical determinant for Drosophila ORC-DNA binding. EMBO J 23, 897-907.
49. Bell SD & Jackson SP (2001) Mechanism and regulation of transcription in archaea. Curr Opin Microbiol 4, 208-213.
50. Kelman LM & Kelman Z (2003) Archaea: an archetype for replication initiation studies? Mol Microbiol 48, 605-616.
51. Lopez P, Philippe H, Myllykallio H & Forterre P (1999) Identification of putative chromosomal origins of replication in Archaea. Mol Micro 32, 883-886.
52. Myllykallio H, Lopez P, Lopez-Garcia P, Heilig R, Saurin W, Zivanovic Y, Philippe H & Forterre P (2000) Bacterial mode of replication with eukaryotic-like machinery in a hyperthermophilic archaeon. Science 288, 2212-2215.
53. Matsunaga F, Norais C, Forterre P & Myllykallio H (2003) Identification of short 'eukaryotic' Okazaki fragments synthesized from a prokaryotic replication origin. EMBO Rep 4, 154-158.
54. Matsunaga F, Forterre P, Ishino Y & Myllykallio H (2001) In vivo interactions of archaeal Cdc6/Orc1 and minichromosome maintenance proteins with the replication origin. Proc Natl Acad Sci USA 98, 11152-11157.
55. Berquist BR & DasSarma S (2003) An archaeal chromosomal autonomously replicating sequence element from an extreme halophile, Halobacterium sp. strain NRC-1. J Bacteriol 185, 5959-5966.
56. Zhang R & Zhang C (2003) Multiple replication origins of the archaeon Halobacterium species NRC-1. Biochem Biophys Res Commun 302, 728-734.
57. Robinson NP, Dionne I, Lundgren M, Marsh VL, Bernander R & Bell SD (2004) Identification of two origins of replication in the single chromosome of the archaeon Sulfolobus solfataricus. Cell 116, 25-38.
58. Capaldi SA & Berger JM (2004) Biochemical characterization of Cdc6/Orc1 binding to the replication origin of the euryarchaeon Methanothermobacter thermoautotrophicus. Nucleic Acids Res 32, 4821-4832.
59. Erzberger JP, Pirruccello MM & Berger JM (2002) The structure of bacterial DnaA: implications for general mechanisms underlying DNA replication initiation. EMBO J 21, 4763-4773.
60. Liu JY, Smith CL, DeRyckere D, DeAngelis K, Martin GS & Berger JM (2000) Structure and function of Cdc6/Cdc18: Implications for origin recognition and checkpoint control. Mol Cell 6, 637-648.
61. Singleton MR, Morales R, Grainge I, Cook N, Isupov MN & Wigley DB (2004) Conformational changes induced by nucleotide binding in Cdc6/ORC from Aeropyrum pernix. J Mol Biol 343, 547-557.
62. Cunningham EL & Berger JM (2005) Unraveling the early steps of prokaryotic replication. Curr Opin Struct Biol 15, 68-76.
63. Lundgren M, Andersson A, Chen LM, Nilsson P & Bernander R (2004) Three replication origins in Sulfolobus species: Synchronous initiation of chromosome replication and asynchronous termination. Proc Natl Acad Sci USA 101, 7046-7051.
64. Bell SD, Botting CH, Wardleworth BN, Jackson SP & White MF (2002) The interaction of Alba, a conserved archaeal, chromatin protein, with Sir2 and its regulation by acetylation. Science 296, 148-151.