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Spontaneous DNA breakage in single living Escherichia coli cells

Nature Genetics volume 39, pages 797802 (2007) | Download Citation

  • A Corrigendum to this article was published on 01 September 2007

This article has been updated


Spontaneous DNA breakage is predicted to be a frequent, inevitable consequence of DNA replication and is thought to underlie much of the genomic change that fuels cancer and evolution1,2,3. Despite its importance, there has been little direct measurement of the amounts, types, sources and fates of spontaneous DNA lesions in living cells. We present a direct, sensitive flow cytometric assay in single living Escherichia coli cells for DNA lesions capable of inducing the SOS DNA damage response, and we report its use in quantification of spontaneous DNA double-strand breaks (DSBs). We report efficient detection of single chromosomal DSBs and rates of spontaneous breakage 20- to 100-fold lower than predicted. In addition, we implicate DNA replication in the origin of spontaneous DSBs with the finding of fewer spontaneous DSBs in a mutant with altered DNA polymerase III. The data imply that spontaneous DSBs induce genomic changes and instability 20–100 times more potently than previously appreciated. Finally, FACS demonstrated two main cell fates after spontaneous DNA damage: viability with or without resumption of proliferation.

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Change history

  • 29 August 2007

    In the version of this article initially published, our estimate of the rate of formation of spontaneous DNA double-strand breaks (DSBs) in E. coli proportional to DNA content in humans should read that it differs from that of Vilenchik and Knudson (Proc. Natl. Acad. Sci. USA 100, 12871–12876; 2003) by fourfold, not 'approximately tenfold' (page 800, line 3, and page 800, line 59). We estimated that there are 0.01 DSBs per E. coli genome replication. Because E. coli has approximately 4.7 x 106 bp per genome (Blattner, F.R. et al., Science 277, 1453–1474; 1997), we estimate that approximately 2 x 10–9 DSBs per bp are replicated, or about fourfold fewer than the estimate of about 0.8 x 10–8 DSBs per bp replicated in human somatic cells (or 50 DSBs per diploid human genome replication) from Vilenchik and Knudson (Proc. Natl. Acad. Sci. USA 100, 12871–12876; 2003). This would bring the number of DSBs per human genome replication down to approximately 13, if it were proportional to that in E. coli. Our error arose from calculating the human equivalent based on haploid, not diploid, human genome size. This error has been corrected in the HTML and PDF versions of the article.


  1. 1.

    et al. The importance of repairing stalled replication forks. Nature 404, 37–41 (2000).

  2. 2.

    Recombinational repair of DNA damage in Escherichia coli and bacteriophage lambda. Microbiol. Mol. Biol. Rev. 63, 751–813 (1999).

  3. 3.

    & Endogenous DNA double-strand breaks: production, fidelity of repair, and induction of cancer. Proc. Natl. Acad. Sci. USA 100, 12871–12876 (2003).

  4. 4.

    et al. DNA Repair and Mutagenesis (American Society for Microbiology, Washington, D.C., 2005).

  5. 5.

    & Structural dynamics of eukaryotic chromosome evolution. Science 301, 793–797 (2003).

  6. 6.

    et al. Measurement of SOS expression in individual Escherichia coli K-12 cells using fluorescence microscopy. Mol. Microbiol. 53, 1343–1357 (2004).

  7. 7.

    , & FACS-optimized mutants of the green fluorescent protein (GFP). Gene 173, 33–38 (1996).

  8. 8.

    , & A switch from high-fidelity to error-prone DNA double-strand break repair underlies stress-induced mutation. Mol. Cell 19, 791–804 (2005).

  9. 9.

    & Characterization of dnaC2 and dnaC28 mutants by flow cytometry. J. Bacteriol. 180, 1624–1631 (1998).

  10. 10.

    , , & Identification of high affinity binding sites for LexA which define new DNA damage-inducible genes in Escherichia coli . J. Mol. Biol. 241, 507–523 (1994).

  11. 11.

    & Sister chromatids are preferred over homologs as substrates for recombinational repair in Saccharomyces cerevisiae . Genetics 132, 387–402 (1992).

  12. 12.

    & Sister chromatid gene conversion is a prominent double-strand break repair pathway in mammalian cells. EMBO J. 19, 3398–3407 (2000).

  13. 13.

    , , & The two Escherichia coli chromosome arms locate to separate cell halves. Genes Dev. 20, 1727–1731 (2006).

  14. 14.

    & Chromosome and replisome dynamics in E. coli: loss of sister cohesion triggers global chromosome movement and mediates chromosome segregation. Cell 121, 899–911 (2005).

  15. 15.

    & The number of sex-factors per chromosome in Escherichia coli . Biochem. J. 121, 93–103 (1971).

  16. 16.

    & Making ends meet: repairing breaks in bacterial DNA by non-homologous end-joining. PLoS Genet. 2, e8 (2006).

  17. 17.

    , , , & Regulation of Saccharomyces Rad53 checkpoint kinase during adaptation from DNA damage-induced G2/M arrest. Mol. Cell 7, 293–300 (2001).

  18. 18.

    , & Replication fork pausing and recombination or “gimme a break”. Genes Dev. 14, 1–10 (2000).

  19. 19.

    , & Mutants of Escherichia coli with increased fidelity of DNA replication. Genetics 134, 1023–1030 (1993).

  20. 20.

    , , , & SOS mutator DNA polymerase IV functions in adaptive mutation and not adaptive amplification. Mol. Cell 7, 571–579 (2001).

  21. 21.

    , , & Multiple pathways process stalled replication forks. Proc. Natl. Acad. Sci. USA 101, 12783–12788 (2004).

  22. 22.

    Suppressing cancer: the importance of being senescent. Science 309, 886–887 (2005).

  23. 23.

    , & RecA protein promotes the regression of stalled replication forks in vitro . Proc. Natl. Acad. Sci. USA 98, 8211–8218 (2001).

  24. 24.

    Bloom syndrome, genomic instability and cancer: the SOS-like hypothesis. Cancer Lett. 236, 1–12 (2006).

  25. 25.

    , , , & On the mechanism of gene amplification induced under stress in Escherichia coli . PLoS Genet. 2, e48 (2006).

  26. 26.

    , & The Escherichia coli mazEF suicide module mediates thymineless death. J. Bacteriol. 185, 1803–1807 (2003).

  27. 27.

    , , & Aging and death in an organism that reproduces by morphologically symmetric division. PLoS Biol. 3, e45 (2005).

  28. 28.

    Aging in bacteria. Curr. Opin. Microbiol. 5, 596–601 (2002).

  29. 29.

    , , & Aging may be a conditional strategic choice and not an inevitable outcome for bacteria. Proc. Natl. Acad. Sci. USA 103, 14831–14835 (2006).

  30. 30.

    & Flow cytometric analysis of microorganisms. Methods Cell Biol. 64, 511–537 (2001).

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We thank the Baylor College of Medicine Flow Cytometry Core and S.A. Sincock and J.P. Robinson (Purdue Cytometry Laboratories) for help with flow cytometry; P.J. Hastings, D.B. Magner, S. Plon and G. Weinstock for discussions and D. Bates, A. Bielinsky, M.M. Cox, C. Herman, M.N. Hersh, G. Ira, M.-J. Lombardo, G.J. McKenzie, X. Pan, R. Rothstein and J.D. Wang for comments on the manuscript. This work was supported by a US Department of Defense Breast Cancer Research Program predoctoral fellowship (J.M.P.) and by US National Institutes of Health grants R01-GM53158 and R01-CA85777, equally.

Author information


  1. Interdepartmental Program in Cell and Molecular Biology and Department of Molecular and Human Genetics, Houston, Texas 77030-3411, USA.

    • Jeanine M Pennington
    •  & Susan M Rosenberg
  2. Department of Biochemistry and Molecular Biology, Department of Molecular Virology and Microbiology and Dan L. Duncan Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030-3411, USA.

    • Susan M Rosenberg


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S.M.R. conceived the study; J.M.P. and S.M.R. designed the study, analyzed the data and wrote the paper and J.M.P. performed the experiments.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Susan M Rosenberg.

Supplementary information

PDF files

  1. 1.

    Supplementary Fig. 1

    One chromosome in most dnaA46(TS) cells at the restrictive temperature.

  2. 2.

    Supplementary Fig. 2

    Chronic SOS induction in dnaA46(TS) cells.

  3. 3.

    Supplementary Fig. 3

    Similar frequencies of spontaneous SOS induction during early, mid- and late-logarithmic phases of growth.

  4. 4.

    Supplementary Fig. 4

    Low frequencies of inviable, propidium iodide-stained cells among spontaneously SOS-induced green cells.

  5. 5.

    Supplementary Table 1

    E. coli K12 strains.

  6. 6.

    Supplementary Methods

  7. 7.

    Supplementary Note

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