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The bacterial DnaA-trio replication origin element specifies single-stranded DNA initiator binding

Nature volume 534, pages 412416 (16 June 2016) | Download Citation

  • An Erratum to this article was published on 29 June 2016

Abstract

DNA replication is tightly controlled to ensure accurate inheritance of genetic information. In all organisms, initiator proteins possessing AAA+ (ATPases associated with various cellular activities) domains bind replication origins to license new rounds of DNA synthesis1. In bacteria the master initiator protein, DnaA, is highly conserved and has two crucial DNA binding activities2. DnaA monomers recognize the replication origin (oriC) by binding double-stranded DNA sequences (DnaA-boxes); subsequently, DnaA filaments assemble and promote duplex unwinding by engaging and stretching a single DNA strand3,4,5. While the specificity for duplex DnaA-boxes by DnaA has been appreciated for over 30 years, the sequence specificity for single-strand DNA binding has remained unknown. Here we identify a new indispensable bacterial replication origin element composed of a repeating trinucleotide motif that we term the DnaA-trio. We show that the function of the DnaA-trio is to stabilize DnaA filaments on a single DNA strand, thus providing essential precision to this binding mechanism. Bioinformatic analysis detects DnaA-trios in replication origins throughout the bacterial kingdom, indicating that this element is part of the core oriC structure. The discovery and characterization of the novel DnaA-trio extends our fundamental understanding of bacterial DNA replication initiation, and because of the conserved structure of AAA+ initiator proteins these findings raise the possibility of specific recognition motifs within replication origins of higher organisms.

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Acknowledgements

We thank J. Errington and W. Vollmer for reviewing the manuscript. We thank G. Scholefield for preliminary data, A. Koh for research assistance and I. Selmes for technical assistance. Research support was provided to H.M. by a Royal Society University Research Fellowship and a Biotechnology and Biological Sciences Research Council Research Grant (BB/K017527/1), and to O.H. by an Iraqi Ministry of Higher Education and Scientific Research Studentship.

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Affiliations

  1. Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4AX, UK

    • Tomas T. Richardson
    • , Omar Harran
    •  & Heath Murray

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Contributions

H.M. and T.T.R. conceived and designed experiments; H.M., T.T.R. and O.H. constructed plasmids and strains; H.M. and O.H. performed growth and marker frequency analysis experiments; H.M. performed microscopy experiments; T.T.R. purified proteins, performed the open complex assay, and performed the DnaA filament formation assays; H.M. and T.T.R. interpreted results and wrote the paper.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Heath Murray.

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https://doi.org/10.1038/nature17962

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