1. Structural Biology and Molecular Biophysics

Two-subunit DNA escort mechanism and inactive subunit bypass in an ultra-fast ring ATPase

  1. Ninning Liu
  2. Gheorghe Chistol
  3. Carlos Bustamante  Is a corresponding author
  1. Harvard University, United States
  2. Harvard Medical School, United States
  3. University of California, Berkeley, United States
https://doi.org/10.7554/eLife.09224
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  1. Ninning Liu
  2. Gheorghe Chistol
  3. Carlos Bustamante
(2015)
Two-subunit DNA escort mechanism and inactive subunit bypass in an ultra-fast ring ATPase
eLife 4:e09224.
https://doi.org/10.7554/eLife.09224
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Abstract

SpoIIIE is a homo-hexameric dsDNA translocase responsible for completing chromosome segregation in B. subtilis. Here we use a single-molecule approach to monitor SpoIIIE translocation when challenged with neutral-backbone DNA and non-hydrolyzable ATP analogs. We show that SpoIIIE makes multiple essential contacts with phosphates on the 5'→3' strand in the direction of translocation. Using DNA constructs with two neutral-backbone segments separated by a single charged base-pair, we deduce that SpoIIIE's step size is 2 bp. Finally, experiments with non-hydrolyzable ATP analogs suggest that SpoIIIE can operate with non-consecutive inactive subunits. We propose a two-subunit escort translocation mechanism that is strict enough to enable SpoIIIE to track one DNA strand, yet sufficiently compliant to permit the motor to bypass inactive subunits without arrest. We speculate that such flexible mechanism arose for motors that, like SpoIIIE, constitute functional bottlenecks where the inactivation of even a single motor can be lethal for the cell.

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Author details

  1. Ninning Liu

    Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, United States
    Competing interests
    The authors declare that no competing interests exist.

  2. Gheorghe Chistol

    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
    Competing interests
    The authors declare that no competing interests exist.

  3. Carlos Bustamante

    Jason L Choy Laboratory of Single Molecule Biophysics, University of California, Berkeley, Berkeley, United States
    For correspondence
    carlosb@berkeley.edu
    Competing interests
    The authors declare that no competing interests exist.

Copyright

© 2015, Liu et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Ninning Liu
  2. Gheorghe Chistol
  3. Carlos Bustamante
(2015)
Two-subunit DNA escort mechanism and inactive subunit bypass in an ultra-fast ring ATPase
eLife 4:e09224.
https://doi.org/10.7554/eLife.09224

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https://doi.org/10.7554/eLife.09224

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    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics

    Mechanochemical coupling and bi-phasic force-velocity dependence in the ultra-fast ring ATPase SpoIIIE

    Ninning Liu, Gheorghe Chistol ... Carlos Bustamante
    Research Advance Updated

    Multi-subunit ring-shaped ATPases are molecular motors that harness chemical free energy to perform vital mechanical tasks such as polypeptide translocation, DNA unwinding, and chromosome segregation. Previously we reported the intersubunit coordination and stepping behavior of the hexameric ring-shaped ATPase SpoIIIE (Liu et al., 2015). Here we use optical tweezers to characterize the motor’s mechanochemistry. Analysis of the motor response to external force at various nucleotide concentrations identifies phosphate release as the likely force-generating step. Analysis of SpoIIIE pausing indicates that pauses are off-pathway events. Characterization of SpoIIIE slipping behavior reveals that individual motor subunits engage DNA upon ATP binding. Furthermore, we find that SpoIIIE’s velocity exhibits an intriguing bi-phasic dependence on force. We hypothesize that this behavior is an adaptation of ultra-fast motors tasked with translocating DNA from which they must also remove DNA-bound protein roadblocks. Based on these results, we formulate a comprehensive mechanochemical model for SpoIIIE.