Molecular Life Sciences

2018 Edition
| Editors: Robert D. Wells, Judith S. Bond, Judith Klinman, Bettie Sue Siler Masters

Replication Origin of E. coli and the Mechanism of Initiation

Reference work entry


The process of DNA replication can be formally divided into the stages of initiation, the elongation of nascent DNA, and termination. In E. coli, DNA replication initiates at a specific location (oriC) on the circular duplex chromosome. This site is where the replication fork machinery is assembled, leading to duplication of the E. coli chromosome. At oriC, specific biochemical events must take place in a step-wise manner in order to establish the enzymatic machinery that will operate at a replication fork. The first step involves the recognition of DNA sequence elements in oriC by the replication initiator (DnaA). Its interaction with these DNA sequences leads to the assembly of a DnaA oligomer that unwinds a region within oriC. DnaA then interacts with DnaB in a complex with DnaC to load the replicative DNA helicase (DnaB) onto the single-stranded DNA in the unwound region. After helicase loading and its activation, involving the binding of primase (DnaG) to DnaB and primer...

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I thank the members of my lab for their support while I wrote. This work is supported by Grant GM090063 from the National Institutes of Health and by the Michigan Agricultural Experiment Station.


  1. Atkinson J, Gupta MK, McGlynn P (2011) Interaction of Rep and DnaB on DNA. Nucleic Acids Res 39(4):1351–1359PubMedCrossRefGoogle Scholar
  2. Barcena M et al (2001) The DnaB.DnaC complex: a structure based on dimers assembled around an occluded channel. EMBO J 20(6):1462–1468PubMedPubMedCentralCrossRefGoogle Scholar
  3. Bates DB et al (1995) The DnaA box R4 in the minimal oriC is dispensable for initiation of Escherichia coli chromosome replication. Nucleic Acids Res 23(16):3119–3125PubMedPubMedCentralCrossRefGoogle Scholar
  4. Bell SP, Kaguni JM (2013) Helicase loading at chromosomal origins of replication. Cold Spring Harb Perspect Biol 5(6):pii:a010124Google Scholar
  5. Boye E et al (1993) Regulation of DNA replication in Escherichia coli. In: Fanning E, Knippers R, Winnacker EL (eds) DNA replication and the cell cycle, vol 43, Mosbacher Kolloquium. Springer, Berlin, pp 15–26CrossRefGoogle Scholar
  6. Bramhill D, Kornberg A (1988) Duplex opening by dnaA protein at novel sequences in initiation of replication at the origin of the E. coli chromosome. Cell 52(5):743–755PubMedCrossRefGoogle Scholar
  7. Brendler T, Austin S (1999) Binding of SeqA protein to DNA requires interaction between two or more complexes bound to separate hemimethylated GATC sequences. EMBO J 18(8):2304–2310PubMedPubMedCentralCrossRefGoogle Scholar
  8. Brendler T, Abeles A, Austin S (1995) A protein that binds to the P1 origin core and the oriC 13mer region in a methylation-specific fashion is the product of the host seqA gene. EMBO J 14(16):4083–4089PubMedPubMedCentralGoogle Scholar
  9. Carr KM, Kaguni JM (2001) Stoichiometry of DnaA and DnaB protein in initiation at the Escherichia coli chromosomal origin. J Biol Chem 276(48):44919–44925PubMedCrossRefGoogle Scholar
  10. Cassler MR, Grimwade JE, Leonard AC (1995) Cell cycle-specific changes in nucleoprotein complexes at a chromosomal replication origin. EMBO J 14(23):5833–5841PubMedPubMedCentralGoogle Scholar
  11. Crooke E et al (1993) Replicatively active complexes of DnaA protein and the Escherichia coli chromosomal origin observed in the electron microscope. J Mol Biol 233(1):16–24PubMedCrossRefGoogle Scholar
  12. Davey MJ et al (2002) The DnaC helicase loader is a dual ATP/ADP switch protein. EMBO J 21(12):3148–3159PubMedPubMedCentralCrossRefGoogle Scholar
  13. Duderstadt KE et al (2010) Origin remodeling and opening in bacteria rely on distinct assembly states of the DnaA initiator. J Biol Chem 285(36):28229–28239PubMedPubMedCentralCrossRefGoogle Scholar
  14. Duderstadt KE, Chuang K, Berger JM (2011) DNA stretching by bacterial initiators promotes replication origin opening. Nature 478(7368):209–213PubMedPubMedCentralCrossRefGoogle Scholar
  15. Erzberger JP, Pirruccello MM, Berger JM (2002) The structure of bacterial DnaA: implications for general mechanisms underlying DNA replication initiation. EMBO J 21(18):4763–4773PubMedPubMedCentralCrossRefGoogle Scholar
  16. Erzberger JP, Mott ML, Berger JM (2006) Structural basis for ATP-dependent DnaA assembly and replication-origin remodeling. Nat Struct Mol Biol 13(8):676–683PubMedCrossRefGoogle Scholar
  17. Fang L, 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(4):541–553PubMedCrossRefGoogle Scholar
  18. Felczak MM, Simmons LA, Kaguni JM (2005) An essential tryptophan of Escherichia coli DnaA protein functions in oligomerization at the E. coli replication origin. J Biol Chem 280(26):24627–24633PubMedCrossRefGoogle Scholar
  19. Finkel SE, Johnson RC (1992) The Fis protein: it’s not just for DNA inversion anymore [published erratum appears in Mol Microbiol 1993 Mar;7(2):1023]. Mol Microbiol 6(22):3257–3265Google Scholar
  20. Flamm EL, Weisberg RA (1985) Primary structure of the hip gene of Escherichia coli and of its product, the beta subunit of integration host factor. J Mol Biol 183(2):117–128PubMedCrossRefGoogle Scholar
  21. 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(3):889–900PubMedCrossRefGoogle Scholar
  22. Galletto R, Jezewska MJ, Bujalowski W (2003) Interactions of the Escherichia coli DnaB helicase hexamer with the replication factor the DnaC protein. Effect of nucleotide cofactors and the ssDNA on protein-protein interactions and the topology of the complex. J Mol Biol 329(3):441–465PubMedCrossRefGoogle Scholar
  23. Gille H, Messer W (1991) Localized DNA melting and structural pertubations in the origin of replication, oriC, of Escherichia coli in vitro and in vivo. EMBO J 10(6):1579–1584PubMedPubMedCentralGoogle Scholar
  24. Gille H et al (1991) The FIS protein binds and bends the origin of chromosomal DNA replication, oriC, of Escherichia coli. Nucleic Acids Res 19(15):4167–4172PubMedPubMedCentralCrossRefGoogle Scholar
  25. Grimwade JE, Ryan VT, Leonard AC (2000) IHF redistributes bound initiator protein, DnaA, on supercoiled oriC of Escherichia coli. Mol Microbiol 35(4):835–844PubMedCrossRefGoogle Scholar
  26. Hiasa H, Marians KJ (1994) Fis cannot support oriC DNA replication in vitro. J Biol Chem 269(40):24999–25003PubMedGoogle Scholar
  27. Hupert-Kocurek K et al (2007) Genetic method to analyze essential genes of Escherichia coli. Appl Environ Microbiol 73(21):7075–7082PubMedPubMedCentralCrossRefGoogle Scholar
  28. 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(32):23083–23086PubMedGoogle Scholar
  29. Jacob F, Monod J (1961) Genetic regulatory mechanisms in the synthesis of proteins. J Mol Biol 3:318–356PubMedCrossRefGoogle Scholar
  30. Jacob F, Brenner S, Cuzin F (1963) On the regulation of DNA replication in bacteria. Cold Spring Harb Symp Quant Biol 28:329–348CrossRefGoogle Scholar
  31. Kano Y, Imamoto F (1990) Requirement of integration host factor (IHF) for growth of Escherichia coli deficient in HU protein. Gene 89(1):133–137PubMedCrossRefGoogle Scholar
  32. Kaur G et al (2014) Building the bacterial orisome: high-affinity DnaA recognition plays a role in setting the conformation of oriC DNA. Mol Microbiol 91(6):1148–1163PubMedPubMedCentralCrossRefGoogle Scholar
  33. Kawakami H, Keyamura K, Katayama T (2005) Formation of an ATP-DnaA-specific initiation complex requires DnaA arginine 285, a conserved motif in the AAA+protein family. J Biol Chem 280(29):27420–27430PubMedCrossRefGoogle Scholar
  34. Keyamura K et al (2009) DiaA dynamics are coupled with changes in initial origin complexes leading to helicase loading. J Biol Chem 284(37):25038–25050PubMedPubMedCentralCrossRefGoogle Scholar
  35. Kim S et al (1996) Coupling of a replicative polymerase and helicase: a tau-DnaB interaction mediates rapid replication fork movement. Cell 84(4):643–650PubMedCrossRefGoogle Scholar
  36. Langer U et al (1996) A comprehensive set of DnaA-box mutations in the replication origin, oriC, of Escherichia coli. Mol Microbiol 21(2):301–311PubMedCrossRefGoogle Scholar
  37. Leonard AC, Grimwade JE (2011) Regulation of DnaA assembly and activity: taking directions from the genome. Annu Rev Microbiol 65:19–35PubMedPubMedCentralCrossRefGoogle Scholar
  38. Ludlam AV et al (2001) Essential amino acids of Escherichia coli DnaC protein in an N-terminal domain interact with DnaB helicase. J Biol Chem 276(29):27345–27353PubMedCrossRefGoogle Scholar
  39. Makowska-Grzyska M, Kaguni JM (2010) Primase directs the release of DnaC from DnaB. Mol Cell 37(1):90–101PubMedPubMedCentralCrossRefGoogle Scholar
  40. Margulies C, Kaguni JM (1996) Ordered and sequential binding of DnaA protein to oriC, the chromosomal origin of Escherichia coli. J Biol Chem 271(29):17035–17040PubMedCrossRefGoogle Scholar
  41. Margulies C, Kaguni JM (1998) The FIS protein fails to block the binding of DnaA protein to oriC, the Escherichia coli chromosomal origin. Nucleic Acids Res 26(22):5170–5175PubMedPubMedCentralCrossRefGoogle Scholar
  42. Marszalek J, Kaguni JM (1994) DnaA protein directs the binding of DnaB protein in initiation of DNA replication in Escherichia coli. J Biol Chem 269(7):4883–4890PubMedGoogle Scholar
  43. Matsui M et al (1985) Sites of dnaA protein-binding in the replication origin of the Escherichia coli K-12 chromosome. J Mol Biol 184(3):529–533PubMedCrossRefGoogle Scholar
  44. McGarry KC et al (2004) Two discriminatory binding sites in the Escherichia coli replication origin are required for DNA strand opening by initiator DnaA-ATP. Proc Natl Acad Sci U S A 101(9):2811–2816PubMedPubMedCentralCrossRefGoogle Scholar
  45. Messer W et al (1992) The complex for replication initiation of Escherichia coli. Chromosoma 102(1 Suppl):S1–S6PubMedCrossRefGoogle Scholar
  46. Mitkova AV, Khopde SM, Biswas SB (2003) Mechanism and stoichiometry of interaction of DnaG primase with DnaB helicase of Escherichia coli in RNA primer synthesis. J Biol Chem 278(52):52253–52261PubMedCrossRefGoogle Scholar
  47. Mott ML et al (2008) Structural synergy and molecular crosstalk between bacterial helicase loaders and replication initiators. Cell 135(4):623–634PubMedPubMedCentralCrossRefGoogle Scholar
  48. Oka A et al (1980) Replication origin of the Escherichia coli K-12 chromosome: the size and structure of the minimum DNA segment carrying the information for autonomous replication. Mol Gen Genet 178(1):9–20PubMedCrossRefGoogle Scholar
  49. Ozaki S, Katayama T (2012) Highly organized DnaA-oriC complexes recruit the single-stranded DNA for replication initiation. Nucleic Acids Res 40(4):1648–1665Google Scholar
  50. Ozaki S et al (2008) A common mechanism for the ATP-DnaA-dependent formation of open complexes at the replication origin. J Biol Chem 283(13):8351–8362PubMedCrossRefGoogle Scholar
  51. Polaczek P (1990) Bending of the origin of replication of E. coli by binding of IHF at a specific site. New Biol 2(3):265–271PubMedGoogle Scholar
  52. Rice PA et al (1996) Crystal structure of an IHF-DNA complex: a protein-induced DNA U-turn. Cell 87(7):1295–1306PubMedCrossRefGoogle Scholar
  53. Rozgaja TA et al (2011) Two oppositely oriented arrays of low-affinity recognition sites in oriC guide progressive binding of DnaA during Escherichia coli pre-RC assembly. Mol Microbiol 82(2):475–488PubMedPubMedCentralCrossRefGoogle Scholar
  54. Ryan VT et al (2002) IHF and HU stimulate assembly of pre-replication complexes at Escherichia coli oriC by two different mechanisms. Mol Microbiol 46(1):113–124PubMedCrossRefGoogle Scholar
  55. Schaper S, Messer W (1995) Interaction of the initiator protein DnaA of Escherichia coli with its DNA target. J Biol Chem 270(29):17622–17626PubMedCrossRefGoogle Scholar
  56. Seitz H, Weigel C, Messer W (2000) The interaction domains of the DnaA and DnaB replication proteins of Escherichia coli. Mol Microbiol 37(5):1270–1279PubMedCrossRefGoogle Scholar
  57. Sekimizu K, Bramhill D, Kornberg A (1987) ATP activates dnaA protein in initiating replication of plasmids bearing the origin of the E. coli chromosome. Cell 50(2):259–265PubMedCrossRefGoogle Scholar
  58. Slater S et al (1995) E. coli SeqA protein binds oriC in two different methyl-modulated reactions appropriate to its roles in DNA replication initiation and origin sequestration. Cell 82(6):927–936PubMedCrossRefGoogle Scholar
  59. Speck C, Messer W (2001) Mechanism of origin unwinding: sequential binding of DnaA to double- and single-stranded DNA. EMBO J 20(6):1469–1476PubMedPubMedCentralCrossRefGoogle Scholar
  60. Stepankiw N et al (2009) The right half of the Escherichia coli replication origin is not essential for viability, but facilitates multi-forked replication. Mol Microbiol 74(2):467–479PubMedPubMedCentralCrossRefGoogle Scholar
  61. Sutton MD et al (1998) E. coli DnaA protein: the N-terminal domain and loading of DnaB helicase at the E. coli chromosomal origin. J Biol Chem 273:34255–34262PubMedCrossRefGoogle Scholar
  62. von Meyenburg K, Hansen FG (1980) The origin of replication, oriC, of the Escherichia coli chromosome: genes near oriC and construction of oriC deletion mutations. ICN-UCLA Symp Mol Cell Biol 19:137–159Google Scholar

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© Springer Science+Business Media, LLC 2018

Authors and Affiliations

  1. 1.Department of Biochemistry and Molecular BiologyMichigan State UniversityEast LansingUSA