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Sequence-directed DNA export guides chromosome translocation during sporulation in Bacillus subtilis

Nature Structural & Molecular Biology volume 15, pages 485–493 (2008)Cite this article

Abstract

In prokaryotes, the transfer of DNA between cellular compartments is essential for the segregation and exchange of genetic material. SpoIIIE and FtsK are AAA+ ATPases responsible for intercompartmental chromosome translocation in bacteria. Despite functional and sequence similarities, these motors were proposed to use drastically different mechanisms: SpoIIIE was suggested to be a unidirectional DNA transporter that exports DNA from the compartment in which it assembles, whereas FtsK was shown to establish translocation directionality by interacting with highly skewed chromosomal sequences. Here we use a combination of single-molecule, bioinformatics and in vivo fluorescence methodologies to study the properties of DNA translocation by SpoIIIE in vitro and in vivo. These data allow us to propose a sequence-directed DNA exporter model that reconciles previously proposed models for SpoIIIE and FtsK, constituting a unified model for directional DNA transport by the SpoIIIE/FtsK family of AAA+ ring ATPases.

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Figure 1: Architecture of SpoIIIE and FtsK monomers and models for DNA translocation directionality.
Figure 2: SpoIIIE-γ is necessary for efficient sporulation but does not affect motor function.
Figure 3: Identification and characterization of a SpoIIIE recognition sequence (SRS).
Figure 4: γ-domains are modular and can be switched between species to confer altered DNA sequence specificities.
Figure 5: Cell-specific GFP tagging indicates that SpoIIIE-Δγ assembles on both sides of the sporulation septum with equal frequency.
Figure 6: Model for SpoIIIE sequence-directed DNA export during sporulation.

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Acknowledgements

The authors would like to dedicate this work to our friend and colleague Nicholas R. Cozzarelli, who passed away during completion of this research. We thank J. Berger for his continuous advice during this research and N. Crisona for critical reading. This work was supported by National Institutes of Health Grants GM31655 (to N.R.C.) and the Human Frontier Science Program (M.N.).

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Author notes

  1. Nicholas R Cozzarelli: Deceased.

  2. Jerod L Ptacin and Marcelo Nollmann: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Molecular and Cell Biology, 642 Stanley Hall, University of California, Berkeley, 94720, California, USA

    Jerod L Ptacin, Marcelo Nollmann & Nicholas R Cozzarelli

  2. Division of Biological Sciences, 4114 Natural Sciences Building, University of California, San Diego, 92093, California, USA

    Eric C Becker & Kit Pogliano

  3. Department of Physics, 231 Birge Hall, University of California, Berkeley, 94720, California, USA

    Carlos Bustamante

  4. Howard Hughes Medical Institute, USA

    Carlos Bustamante

  5. Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, 94720, California, USA

    Carlos Bustamante

Authors
  1. Jerod L Ptacin
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  4. Nicholas R Cozzarelli
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  5. Kit Pogliano
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Contributions

J.L.P. and M.N. planned, collected and interpreted single-molecule, biochemical and fluorescence data; E.C.B. performed time-lapse fluorescence studies of SpoIIIE-SK chimera and compartment-specific GFP-tagging experiments; J.L.P., M.N., E.C.B., K.P. and C.B. wrote the paper.

Corresponding author

Correspondence to Carlos Bustamante.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–6, Supplementary Tables 1–3, Supplementary Results and Supplementary Methods (PDF 1665 kb)

Supplementary Video 1

DNA is forward translocated into forespore compartment in all events tracked (N=28) and all cells observed (N=243). (MOV 3687 kb)

Supplementary Video 2

Frequently, DNA is initially translocated into the forespore followed by a pause in translocation and subsequent reversal of DNA translocation direction that pumps the chromosome out of the forespore compartment (N=140 out of 349 cells). (MOV 3251 kb)

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Ptacin, J., Nollmann, M., Becker, E. et al. Sequence-directed DNA export guides chromosome translocation during sporulation in Bacillus subtilis. Nat Struct Mol Biol 15, 485–493 (2008). https://doi.org/10.1038/nsmb.1412

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