Intersubunit coordination in a homomeric ring ATPase

Abstract

Homomeric ring ATPases perform many vital and varied tasks in the cell, ranging from chromosome segregation to protein degradation. Here we report the direct observation of the intersubunit coordination and step size of such a ring ATPase, the double-stranded-DNA packaging motor in the bacteriophage ϕ29. Using high-resolution optical tweezers, we find that packaging occurs in increments of 10 base pairs (bp). Statistical analysis of the preceding dwell times reveals that multiple ATPs bind during each dwell, and application of high force reveals that these 10-bp increments are composed of four 2.5-bp steps. These results indicate that the hydrolysis cycles of the individual subunits are highly coordinated by means of a mechanism novel for ring ATPases. Furthermore, a step size that is a non-integer number of base pairs demands new models for motor–DNA interactions.

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Figure 1: Bacteriophage ϕ29 packages DNA in bursts of 10 bp.
Figure 2: Dwells before 10-bp bursts contain multiple kinetic events.
Figure 3: The 10-bp bursts are composed of four 2.5-bp steps.
Figure 4: Intersubunit coordination in the ring ATPase of ϕ29.
Figure 5: Packaging models that produce a non-integer step size.

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Acknowledgements

We thank C. L. Hetherington, M. Nollmann and G. Chistol for a critical reading of the manuscript; C. L. Hetherington, A. Politzer, M. Strycharska, M. Kopaczynska and J. Yu for critical discussions; and J. Choy, S. Grill and S. Smith for advice regarding instrumentation. J.R.M. acknowledges the National Science Foundation’s Graduate Research Fellowship and Y.R.C. the Burroughs Welcome Fund’s Career Awards at the Scientific Interface for funding. This research was supported in part by NIH grants GM-071552, DE-003606 and GM-059604. The content of this paper is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

Author Contributions J.R.M., Y.R.C. and K.A. conducted the experiments and performed the analysis; S.G., P.J.J. and D.L.A. prepared and provided experimental materials; and J.R.M., Y.R.C., K.A., S.G., P.J.J., D.L.A. and C.B. wrote the paper. J.R.M. and Y.R.C. contributed equally to this work.

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Correspondence to Carlos Bustamante.

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Moffitt, J., Chemla, Y., Aathavan, K. et al. Intersubunit coordination in a homomeric ring ATPase. Nature 457, 446–450 (2009). https://doi.org/10.1038/nature07637

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