Letter | Published:

DNA replication fidelity in Mycobacterium tuberculosis is mediated by an ancestral prokaryotic proofreader

Nature Genetics volume 47, pages 677681 (2015) | Download Citation

Abstract

The DNA replication machinery is an important target for antibiotic development in increasingly drug-resistant bacteria, including Mycobacterium tuberculosis1. Although blocking DNA replication leads to cell death, disrupting the processes used to ensure replication fidelity can accelerate mutation and the evolution of drug resistance. In Escherichia coli, the proofreading subunit of the replisome, the ɛ exonuclease, is essential for high-fidelity DNA replication2; however, we find that the corresponding subunit is completely dispensable in M. tuberculosis. Rather, the mycobacterial replicative polymerase DnaE1 itself encodes an editing function that proofreads DNA replication, mediated by an intrinsic 3′–5′ exonuclease activity within its PHP domain. Inactivation of the DnaE1 PHP domain increases the mutation rate by more than 3,000-fold. Moreover, phylogenetic analysis of DNA replication proofreading in the bacterial kingdom suggests that E. coli is a phylogenetic outlier and that PHP domain–mediated proofreading is widely conserved and indeed may be the ancestral prokaryotic proofreader.

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Acknowledgements

We thank E. Rubin, B. Bloom, D. Boyd, J. McKenzie, D. Warner and B. Javid for comments, B. Jacobs (Albert Einstein College of Medicine) and M. Wilmans (European Molecular Biology Laboratory) for bacterial strains, and T. Baker (University of Auckland) for plasmids. This work was supported by a Helen Hay Whitney fellowship to J.M.R., US National Institutes of Health Director's New Innovator Award 1DP20D001378, subcontracts from National Institute of Allergy and Infectious Diseases (NIAID) U19AI076217 and AI109755-01, the Doris Duke Charitable Foundation under grant 2010054 to S.M.F. and a UK Medical Research Council grant to M.H.L. (MC_U105197143).

Author information

Author notes

    • Jeremy M Rock
    •  & Ulla F Lang

    These authors contributed equally to this work.

    • Sarah M Fortune
    •  & Meindert H Lamers

    These authors jointly supervised this work.

Affiliations

  1. Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, USA.

    • Jeremy M Rock
    • , Michael R Chase
    • , Christopher B Ford
    • , Elias R Gerrick
    • , Richa Gawande
    •  & Sarah M Fortune
  2. Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge, UK.

    • Ulla F Lang
    •  & Meindert H Lamers
  3. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.

    • Christopher B Ford
    •  & Sarah M Fortune
  4. Swiss Tropical and Public Health Institute, Basel, Switzerland.

    • Mireia Coscolla
    •  & Sebastien Gagneux
  5. University of Basel, Basel, Switzerland.

    • Mireia Coscolla
    •  & Sebastien Gagneux
  6. Ragon Institute of Massachusetts General Hospital, Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.

    • Sarah M Fortune

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Contributions

J.M.R., U.F.L., M.H.L. and S.M.F. designed the project and wrote the manuscript. M.R.C. performed phylogenetic analyses. C.B.F. and E.R.G. made strains and measured mutation rates. R.G., M.C. and S.G. contributed sequencing data.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Sarah M Fortune or Meindert H Lamers.

Integrated supplementary information

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–7 and Supplementary Tables 5–7.

Excel files

  1. 1.

    Supplementary Table 1

    dnaE1 (Rv1547 ) PHP domain SNPs in clinical M. tuberculosis isolates.

  2. 2.

    Supplementary Table 2

    Protein sequences used in phylogenetic analysis.

  3. 3.

    Supplementary Table 3

    HMMER comparison of ε hoologs to TIGR01406 (dnaQ_proteo).

  4. 4.

    Supplementary Table 4

    Drug minimum inhibitory concentrations (μg/ml).

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DOI

https://doi.org/10.1038/ng.3269

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