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Analysis of DNA supercoil induction by FtsK indicates translocation without groove-tracking

Nature Structural & Molecular Biology volume 12, pages 436–440 (2005)Cite this article

Abstract

FtsK is a bacterial protein that translocates DNA in order to transport chromosomes within the cell. During translocation, DNA's double-helical structure might cause a relative rotation between FtsK and the DNA. We used a single-molecule technique to quantify this rotation by observing the supercoils induced into the DNA during translocation of an FtsK complex. We find that FtsK induces ∼0.07 supercoils per DNA helical pitch traveled. This rate indicates that FtsK does not track along DNA's groove, but it is consistent with our previous estimate of FtsK's step size. We show that this rate of supercoil induction is markedly near to the ideal value that would minimize in vivo disturbance to the chromosomal supercoil density, suggesting an origin for the unusual rotational behavior of FtsK.

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Figure 1: Stretching and supercoiling a single DNA molecule.
Figure 2: FtsK50C translocation events on supercoiled DNA.
Figure 3: A histogram of κ values computed from each of 92 events.
Figure 4: Possible FtsK50C translocation mechanism.

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References

  1. Liu, L.F. & Wang, J.C. Supercoiling of the DNA template during transcription. Proc. Natl. Acad. Sci. USA 84, 7024–7027 (1987).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Yang, L., Jessee, C.B., Lau, K., Zhang, H. & Liu, L.F. Template supercoiling during ATP-dependent DNA helix tracking—studies with simian virus-40 large tumor antigen. Proc. Natl. Acad. Sci. USA 86, 6121–6125 (1989).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Tsao, Y.P., Wu, H.Y. & Liu, L.F. Transcription-driven supercoiling of DNA—direct biochemical evidence from in vitro studies. Cell 56, 111–118 (1989).

    Article  CAS  PubMed  Google Scholar 

  4. Koo, H.S., Claassen, L., Grossman, L. & Liu, L.F. ATP-dependent partitioning of the DNA template into supercoiled domains by Escherichia coli UvrAB. Proc. Natl. Acad. Sci. USA 88, 1212–1216 (1991).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Janscak, P. & Bickle, T.A. DNA supercoiling during ATP-dependent DNA translocation by the type I restriction enzyme EcoAl. J. Mol. Biol. 295, 1089–1099 (2000).

    Article  CAS  PubMed  Google Scholar 

  6. Harada, Y. et al. Direct observation of DNA rotation during transcription by Escherichia coli RNA polymerase. Nature 409, 113–115 (2001).

    Article  CAS  PubMed  Google Scholar 

  7. Seidel, R. et al. Real-time observation of DNA translocation by the type I restriction modification enzyme EcoR124I. Nat. Struct. Mol. Biol. 11, 838–843 (2004).

    Article  CAS  PubMed  Google Scholar 

  8. Lesterlin, C., Barre, F.-X. & Cornet, F. Genetic recombination and the cell cycle: what we have learned from chromosome dimers. Mol. Microbiol. 54, 1151–1160 (2004).

    Article  CAS  PubMed  Google Scholar 

  9. Aussel, L. et al. FtsK is a DNA motor protein that activates chromosome dimer resolution by switching the catalytic state of the XerC and XerD recombinases. Cell 108, 195–205 (2002).

    Article  CAS  PubMed  Google Scholar 

  10. Lau, I.F. et al. Spatial and temporal organization of replicating Escherichia coli chromosomes. Mol. Microbiol. 49, 731–743 (2003).

    Article  CAS  PubMed  Google Scholar 

  11. Saleh, O.A., Perals, C., Barre, F.-X. & Allemand, J.-F. Fast, DNA-sequence independent translocation by FtsK in a single-molecule experiment. EMBO J. 23, 2430–2439 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Champoux, J.J. DNA topoisomerases: structure, function, and mechanism. Annu. Rev. Biochem. 70, 369–413 (2001).

    Article  CAS  PubMed  Google Scholar 

  13. Ip, S.C.Y., Bregu, M., Barre, F.-X. & Sherratt, D.J. Decatenation of DNA circles by FtsK-dependent Xer site-specific recombination. EMBO J. 22, 6399–6407 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Pease, P.J. et al. Sequence-directed DNA translocation by purified FtsK. Science 307, 586–590 (2005).

    Article  CAS  PubMed  Google Scholar 

  15. Strick, T.R., Allemand, J.-F., Bensimon, D., Bensimon, A. & Croquette, V. The elasticity of a single supercoiled DNA molecule. Science 271, 1835–1837 (1996).

    Article  CAS  PubMed  Google Scholar 

  16. Strick, T.R., Allemand, J.-F., Bensimon, D. & Croquette, V. Behavior of supercoiled DNA. Biophys. J. 74, 2016–2028 (1998).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Sase, I., Miyata, H., Ishiwata, S. & Kinosita, K. Axial rotation of sliding actin filaments revealed by single-fluorophore imaging. Proc. Natl. Acad. Sci. USA 94, 5646–5650 (1997).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Ali, M.Y. et al. Myosin V is a left-handed spiral motor on the right-handed actin helix. Nat. Struct. Biol. 9, 464–467 (2002).

    Article  CAS  PubMed  Google Scholar 

  19. Singleton, M.R., Sawaya, M.R., Ellenberger, T. & Wigley, D.B. Crystal structure of T7 gene 4 ring helicase indicates a mechanism for sequential hydrolysis of nucleotides. Cell 101, 589–600 (2000).

    Article  CAS  PubMed  Google Scholar 

  20. Hishida, T., Han, Y.-W., Fujimoto, S., Iwasaki, H. & Shinagawa, H. Direct evidence that a conserved arginine in RuvB AAA+ ATPase acts as an allosteric effector for the ATPase activity of the adjacent subunit in a hexamer. Proc. Natl. Acad. Sci. USA 101, 9573–9577 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Wang, J.C. DNA supercoiling and its effects on the structure of DNA. J. Cell Sci., 21–29 (1984).

  22. Zechiedrich, E.L. et al. Roles of topoisomerases in maintaining steady-state DNA supercoiling in Escherichia coli. J. Biol. Chem. 275, 8103–8113 (2000).

    Article  CAS  PubMed  Google Scholar 

  23. Bath, J., Wu, L.J., Errington, J. & Wang, J.C. Role of Bacillus subtilis SpoIIIE in DNA transport across the mother cell-prespore division septum. Science 290, 995–997 (2000).

    Article  CAS  PubMed  Google Scholar 

  24. Perals, K., Cornet, F., Merlet, Y., Delon, I. & Louarn, J.M. Functional polarization of the Escherichia coli chromosome terminus: the dif site acts in chromosome dimer resolution only when located between long stretches of opposite polarity. Mol. Microbiol. 36, 33–43 (2000).

    Article  CAS  PubMed  Google Scholar 

  25. Bouchiat, C. et al. Estimating the persistence length of a worm-like chain molecule from force-extension measurements. Biophys. J. 76, 409–413 (1999).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Efron, B. & Tibshirani, R. Statistical data analysis in the computer age. Science 253, 390–395 (1991).

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

We thank D. Bensimon and V. Croquette for helpful discussions, and K. Neuman for critical reading of the manuscript. This work was supported by the DRAB 2004 program. Research in Paris was also supported by grants from the ACI Jeune Chercheur program and from the European Union MolSwitch program. Research in Toulouse was also supported by grants from the Centre National de la Recherche Scientifique ATIP program and from the French Research Ministry Fundamental Microbiology ACI program.

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Authors and Affiliations

  1. Laboratoire de Physique Statistique et Département de Biologie, Ecole Normale Supérieure, UMR8550 associé au CNRS et aux Universités Paris VI et VII, Paris, France

    Omar A Saleh & Jean-François Allemand

  2. Laboratoire de Microbiologie et de Génétique Moléculaire, CNRS UMR5100, Toulouse, France

    Sarah Bigot & François-Xavier Barre

  3. Centre de Génétique Moléculaire, CNRS UPR2167, Gif-sur-Yvette, France

    François-Xavier Barre

  4. Département de Chimie, Laboratoire Pasteur, Ecole Normale Supérieure, Paris, France

    Jean-François Allemand

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  1. Omar A Saleh
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  2. Sarah Bigot
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  4. Jean-François Allemand
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Correspondence to Omar A Saleh.

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Supplementary information

Supplementary Fig. 1

Slipping by FtsK50C near the positive buckling threshold. (PDF 41 kb)

Supplementary Fig. 2

DNA topology changes induced by FtsK50C translocation. (PDF 138 kb)

Supplementary Methods (PDF 30 kb)

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Saleh, O., Bigot, S., Barre, FX. et al. Analysis of DNA supercoil induction by FtsK indicates translocation without groove-tracking. Nat Struct Mol Biol 12, 436–440 (2005). https://doi.org/10.1038/nsmb926

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