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Vps4 disassembles an ESCRT-III filament by global unfolding and processive translocation

Nature Structural & Molecular Biology volume 22, pages 492–498 (2015)Cite this article

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Abstract

The AAA+ ATPase Vps4 disassembles ESCRT-III and is essential for HIV-1 budding and other pathways. Vps4 is a paradigmatic member of a class of hexameric AAA+ ATPases that disassemble protein complexes without degradation. To distinguish between local displacement versus global unfolding mechanisms for complex disassembly, we carried out hydrogen/deuterium exchange during Saccharomyces cerevisiae Vps4 disassembly of a chimeric Vps24-2 ESCRT-III filament. EX1 exchange behavior shows that Vps4 completely unfolds ESCRT-III substrates on a time scale consistent with the disassembly reaction. The established unfoldase ClpX showed the same pattern, thus demonstrating a common unfolding mechanism. Vps4 hexamers containing a single cysteine residue in the pore loops were cross-linked to ESCRT-III subunits containing unique cysteines within the folded core domain. These data support a mechanism in which Vps4 disassembles its substrates by completely unfolding them and threading them through the central pore.

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Figure 1: Dynamics of a model ESCRT-III substrate of Vps4.
Figure 2: Vps4 completely unfolds ESCRT-III substrate in the course of disassembly.
Figure 3: Vps4 unfolds the Vps24-2 part of MBP–Vps24-2–ssrA as efficiently as ClpX.
Figure 4: Unfolding of MBP–Vps24-2–ssrA by ClpX and Vps4.
Figure 5: Pore-loop residues are required for disassembly.
Figure 6: ATP-dependent cross-linking of Vps24-2 to the central pore.

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Acknowledgements

We thank K. Nyquist (University of California, Berkeley) for samples of Escherichia coli ClpX and ClpP. This work was supported by grants R01AI112442 (J.H.H.) and R01GM094497 (A.M.) from the US National Institutes of Health.

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Authors and Affiliations

  1. Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA.,

    Bei Yang, Goran Stjepanovic, Qingtao Shen, Andreas Martin & James H Hurley

  2. Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA

    James H Hurley

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Contributions

B.Y. conceived the project, created reagents, acquired data, analyzed data and wrote the manuscript; G.S. analyzed data; Q.S. acquired data; A.M. conceived the project and wrote the manuscript; J.H.H. conceived the project, analyzed data and wrote the manuscript.

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Correspondence to James H Hurley.

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Integrated supplementary information

Supplementary Figure 1 Vps24-2 filaments.

(a) Electron micrograph of negatively stained filaments of Vps24-2. Scale bar = 50 nm. (b) Sedimentation of Vps24-2 and MBP-Vps24-2-ssrA. Vps24-2 and MBP-Vps24-2-ssrA were concentrated to above 200 μM and incubated at 4 oC overnight before dilution to 5 μM and ultracentrifugation. The resulting pellet (P) and supernatant (S) fractions were analyzed by SDS-PAGE.

Supplementary Figure 2 Peptide coverage of Vps24-2 and MBP–Vps24-2–ssrA.

Sequence coverage map for (a) Vps24-2 and (b) MBP-Vps24-2-ssrA. Solid green lines above the protein sequence denote the pepsin digest fragments identified in the study. The two residues mutated to cysteine for crosslinking experiments are labeled with asterisks.

Supplementary Figure 3 Filamentous Vps24-2 has a stable core.

(a) Total deuteron incorporation into undigested Vps24-2 monomers (triangles) and filaments (squares) over time. (b) Deuteron incorporation over time for the Vps24-2 part of MBP-Vps24-2-ssrA, mapped onto the Vps24-2 structural model. (c) and (d) Deuteron incorporation at 5 sec, 20 sec, 2min and 5 min for Vps24-2 monomers (c) and Vps24-2 filaments (d), mapped onto the Vps24-2 structural model. The color-coding for different percentages of deuteron incorporation is the same as in Fig. 2b.

Supplementary Figure 4 Vps4-dependent EX1 exchange in helices α1, α2 and α3.

(a), (c) and (e) Mass spectra of the indicated peptides from helices α1, α2, and α3 of Vps24-2 monomers (left), filaments (middle) or filaments plus Vps4 (right). Controls and time points are indicated. Arrows above the spectra indicate regions of the spectrum representing EX2 and EX1 behavior. (b), (d) and (f) Peak-width analysis of the selected peptides at 5, 10, 20, 30, 40 and 60 sec. Open circles, Vps24-2 monomers; filled squares, Vps24-2 filaments; filled triangles, Vps24-2 filaments plus Vps4. The grey bar denotes the 2 Da peak-width change allowance for peptides undergoing EX2 kinetics 41. Each peptide is color coded as in Fig. 2a.

Supplementary Figure 5 ClpX- and Vps4-dependent EX1 exchange in MBP.

(a-d) Mass spectra of four additional peptides from the MBP portion of MBP-Vps24-2-ssrA prior to incubation in D2O (top row), alone (second row), and in the presence of ClpX (third row) or Vps4 (fourth row), or after unfolding in 6 M GdnHCl followed by complete deuteration (bottom row). Each peptide is color coded as in Fig. 4a.

Supplementary Figure 6 ATPase activity of Vps4 constructs.

(a) SDS-PAGE gel of Vps4CF-mediated disassembly of Vps24-2 filament. (b) Bar graph showing the ATPase activity of Vps4 constructs in the absence or presence of substrate Vps24-2. (c) Structural model of Vps24 with position of I92C and M136C mutation highlighted in yellow.

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Supplementary Data Set 1

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Yang, B., Stjepanovic, G., Shen, Q. et al. Vps4 disassembles an ESCRT-III filament by global unfolding and processive translocation. Nat Struct Mol Biol 22, 492–498 (2015). https://doi.org/10.1038/nsmb.3015

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