Letter | Published:

Accelerated growth in the absence of DNA replication origins

Nature volume 503, pages 544547 (28 November 2013) | Download Citation


DNA replication initiates at defined sites called origins, which serve as binding sites for initiator proteins that recruit the replicative machinery. Origins differ in number and structure across the three domains of life1 and their properties determine the dynamics of chromosome replication. Bacteria and some archaea replicate from single origins, whereas most archaea and all eukaryotes replicate using multiple origins. Initiation mechanisms that rely on homologous recombination operate in some viruses. Here we show that such mechanisms also operate in archaea. We use deep sequencing to study replication in Haloferax volcanii and identify four chromosomal origins of differing activity. Deletion of individual origins results in perturbed replication dynamics and reduced growth. However, a strain lacking all origins has no apparent defects and grows significantly faster than wild type. Origin-less cells initiate replication at dispersed sites rather than at discrete origins and have an absolute requirement for the recombinase RadA, unlike strains lacking individual origins. Our results demonstrate that homologous recombination alone can efficiently initiate the replication of an entire cellular genome. This raises the question of what purpose replication origins serve and why they have evolved.

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Gene Expression Omnibus

Data deposits

Sequencing data have been submitted to NCBI Gene Expression Omnibus under accession number GSE41961.


  1. 1.

    & Origins of DNA replication in the three domains of life. FEBS J. 272, 3757–3766 (2005)

  2. 2.

    et al. The complete genome sequence of Haloferax volcanii DS2, a model archaeon. PLoS ONE 5, e9605 (2010)

  3. 3.

    , , & Model organisms for genetics in the domain Archaea: methanogens, halophiles, Thermococcales and Sulfolobales. FEMS Microbiol. Rev. 35, 577–608 (2011)

  4. 4.

    et al. Genetic and physical mapping of DNA replication origins in Haloferax volcanii. PLoS Genet. 3, e77 (2007)

  5. 5.

    & Conservation of replication timing reveals global and local regulation of replication origin activity. Genome Res. 22, 1953–1962 (2012)

  6. 6.

    & Identification of replication origins in prokaryotic genomes. Brief. Bioinform. 9, 376–391 (2008)

  7. 7.

    , , & Mathematical modelling of whole chromosome replication. Nucleic Acids Res. 38, 5623–5633 (2010)

  8. 8.

    , & Replication termination and chromosome dimer resolution in the archaeon Sulfolobus solfataricus. EMBO J. 30, 145–153 (2011)

  9. 9.

    , & Dynamics of DNA replication in yeast. Phys. Rev. Lett. 107, 068103 (2011)

  10. 10.

    , & Chromosome replication dynamics in the archaeon Sulfolobus acidocaldarius. Proc. Natl Acad. Sci. USA 105, 16737–16742 (2008)

  11. 11.

    , , & Genome-wide detection of chromosomal rearrangements, indels, and mutations in circular chromosomes by short read sequencing. Genome Res. 21, 1388–1393 (2011)

  12. 12.

    & The cell cycle of archaea. Nature Rev. Microbiol. 11, 627–638 (2013)

  13. 13.

    et al. Linear derivatives of Saccharomyces cerevisiae chromosome III can be maintained in the absence of autonomously replicating sequence elements. Mol. Cell. Biol. 27, 4652–4663 (2007)

  14. 14.

    , & Activation of silent replication origins at autonomously replicating sequence elements near the HML locus in budding yeast. Mol. Cell. Biol. 19, 6098–6109 (1999)

  15. 15.

    et al. Sequence-independent DNA binding and replication initiation by the human origin recognition complex. Genes Dev. 17, 1894–1908 (2003)

  16. 16.

    Stable DNA replication: interplay between DNA replication, homologous recombination, and transcription. Microbiol. Mol. Biol. Rev. 61, 212–238 (1997)

  17. 17.

    & Initiation of bacteriophage T4 DNA replication and replication fork dynamics: a review in the Virology Journal series on bacteriophage T4 and its relatives. Virol. J. 7, 358 (2010)

  18. 18.

    , & The conflict between DNA replication and transcription. Mol. Microbiol. 85, 12–20 (2012)

  19. 19.

    et al. UV irradiation induces homologous recombination genes in the model archaeon, Halobacterium sp. NRC-1. Saline Syst. 1, 3 (2005)

  20. 20.

    & Construction and analysis of a recombination-deficient (radA) mutant of Haloferax volcanii. Mol. Microbiol. 23, 791–797 (1997)

  21. 21.

    , , & Mre11-Rad50 promotes rapid repair of DNA damage in the polyploid archaeon Haloferax volcanii by restraining homologous recombination. PLoS Genet. 5, e1000552 (2009)

  22. 22.

    et al. Characterization of a tightly controlled promoter of the halophilic archaeon Haloferax volcanii and its use in the analysis of the essential cct1 gene. Mol. Microbiol. 66, 1092–1106 (2007)

  23. 23.

    , , & RNase H confers specificity in the dnaA-dependent initiation of replication at the unique origin of the Escherichia coli chromosome in vivo and in vitro. Proc. Natl Acad. Sci. USA 81, 1040–1044 (1984)

  24. 24.

    et al. Genomewide and biochemical analyses of DNA-binding activity of Cdc6/Orc1 and Mcm proteins in Pyrococcus sp. Nucleic Acids Res. 35, 3214–3222 (2007)

  25. 25.

    , , & Replisome stall events have shaped the distribution of replication origins in the genomes of yeasts. Nucleic Acids Res. . (19 August 2013)

  26. 26.

    , , & Regulated polyploidy in halophilic archaea. PLoS ONE 1, e92 (2006)

  27. 27.

    et al. Genome-wide genetic analysis of polyploidy in yeast. Nature 443, 541–547 (2006)

  28. 28.

    , & The mechanism of DNA transfer in the mating system of an archaebacterium. Science 245, 1387–1389 (1989)

  29. 29.

    & Extra-chromosomal elements and the evolution of cellular DNA replication machineries. Nature Rev. Mol. Cell Biol. 9, 569–574 (2008)

  30. 30.

    , , & Development of additional selectable markers for the halophilic archaeon Haloferax volcanii based on the leuB and trpA genes. Appl. Environ. Microbiol. 70, 943–953 (2004)

  31. 31.

    & Microbial selection. Science 116, 45–51 (1952)

  32. 32.

    , & DNA damage induces nucleoid compaction via the Mre11-Rad50 complex in the archaeon Haloferax volcanii. Mol. Microbiol. 87, 168–179 (2013)

  33. 33.

    , , , & Improved strains and plasmid vectors for conditional overexpression of His-tagged proteins in Haloferax volcanii. Appl. Environ. Microbiol. 76, 1759–1769 (2010)

  34. 34.

    et al. Personalized copy number and segmental duplication maps using next-generation sequencing. Nature Genet. 41, 1061–1067 (2009)

  35. 35.

    , , & Mapping of active replication origins in vivo in thaum- and euryarchaeal replicons. Mol. Microbiol.. (16 September 2013)

  36. 36.

    & Halobacterium volcanii spec. nov., a Dead Sea halobacterium with a moderate salt requirement. Arch. Microbiol. 104, 207–214 (1975)

  37. 37.

    , & A new simvastatin (mevinolin)-resistance marker from Haloarcula hispanica and a new Haloferax volcanii strain cured of plasmid pHV2. Microbiology 147, 959–964 (2001)

  38. 38.

    , & The archaeal Xpf/Mus81/FANCM homolog Hef and the Holliday junction resolvase Hjc define alternative pathways that are essential for cell viability in Haloferax volcanii. DNA Repair 9, 994–1002 (2010)

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This work was supported through the Biotechnology and Biological Sciences Research Council (BBSRC) (BB/E023754/1, BB/G001596/1). We thank the BBSRC for a David Phillips Fellowship awarded to C.A.N. and the Royal Society for a University Research Fellowship awarded to T.A., R. Wilson for preparing libraries for sequencing, A. de Moura and I. Duggin for sharing unpublished data, and numerous colleagues for discussions.

Author information

Author notes

    • Michelle Hawkins
    • , Conrad A. Nieduszynski
    •  & Thorsten Allers

    These authors contributed equally to this work.


  1. School of Biology, University of Nottingham, Queen’s Medical Centre, Nottingham NG7 2UH, UK

    • Michelle Hawkins
    • , Conrad A. Nieduszynski
    •  & Thorsten Allers
  2. Deep Seq, University of Nottingham, Queen’s Medical Centre, Nottingham NG7 2UH, UK

    • Sunir Malla
    •  & Martin J. Blythe


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M.H., C.A.N. and T.A. conceived and designed experiments; M.H. and T.A. performed experiments; S.M. prepared libraries for sequencing; M.J.B. aligned sequencing data to the genome; C.A.N. analysed sequencing data; M.H., C.A.N. and T.A. interpreted results and wrote the paper.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Conrad A. Nieduszynski or Thorsten Allers.

Extended data

Supplementary information

Excel files

  1. 1.

    Supplementary Table 1

    This file shows the deep sequencing data, it contains the following data from each experiment: chromosome or mega-plasmid, mid-point of 1 kb windows used, GC proportion for 1 kb windows, sequence reads for stationary and exponential phase samples, ratio of exponential to stationary phase sequence reads, normalized ratio, genomic co-ordinates for the reconstructed main chromosome.

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