Letter | Published:

Accelerated growth in the absence of DNA replication origins

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

Abstract

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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Accessions

Gene Expression Omnibus

Data deposits

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

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Acknowledgements

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Fellowship awarded to T.A., R. Wilson for preparing libraries for sequencing, A. de Moura and I. Duggin for sharing unpublished data, and numerous colleagues for discussions.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.

Affiliations

  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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Contributions

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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DOI

https://doi.org/10.1038/nature12650

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