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Molecular architecture of the chick vestibular hair bundle

Nature Neuroscience volume 16, pages 365–374 (2013)Cite this article

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Abstract

Hair bundles of the inner ear have a specialized structure and protein composition that underlies their sensitivity to mechanical stimulation. Using mass spectrometry, we identified and quantified >1,100 proteins, present from a few to 400,000 copies per stereocilium, from purified chick bundles; 336 of these were significantly enriched in bundles. Bundle proteins that we detected have been shown to regulate cytoskeleton structure and dynamics, energy metabolism, phospholipid synthesis and cell signaling. Three-dimensional imaging using electron tomography allowed us to count the number of actin-actin cross-linkers and actin-membrane connectors; these values compared well to those obtained from mass spectrometry. Network analysis revealed several hub proteins, including RDX (radixin) and SLC9A3R2 (NHERF2), which interact with many bundle proteins and may perform functions essential for bundle structure and function. The quantitative mass spectrometry of bundle proteins reported here establishes a framework for future characterization of dynamic processes that shape bundle structure and function.

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Figure 1: Quantitative analysis of chick hair-bundle proteins.
Figure 2: Protein composition of chick hair bundles.
Figure 3: Electron tomography of chick stereocilia.
Figure 4: Interaction network for hair-bundle proteins.
Figure 5: Identification of RDX and SLC9A3R2 in hair bundles.

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Acknowledgements

Mass spectrometry was carried out by the W.M. Keck Biomedical Mass Spectrometry Laboratory and The University of Virginia Biomedical Research Facility. We thank K. McDonald, R. Zalpuri and G. Min of the University of California Berkeley Electron Microscopy Laboratory for assistance with high-pressure freezing and imaging; D. Jorgens provided mentoring in high-pressure freezing. We would like to thank A. Cheng, B. Carragher and C. Potter for help with electron microscopy data collection at the National Resource for Automated Molecular Microscopy, supported by US National Institutes of Health (NIH) National Center for Research Resources grant RR017573. For technical assistance, we acknowledge A. Snyder of the Advanced Light Microscopy Core at The Jungers Center (Oregon Health & Science University), supported by shared instrumentation grants S10 RR023432 and S10 RR025440 from the National Center for Research Resources (NIH). Work described here was supported by NIH grants K99/R00 DC009412 (J.B.S.), F32 DC012455 (J.F.K.), R01 DC002368 (P.G.B.-G.), R01 DC011034 (P.G.B.-G.), P30 DC005983 (P.G.B.-G.), R01 EY007755 (L.L.D.), P30 EY10572 (L.L.D.) and P01 GM051487 (M.A.).

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Author notes

  1. Jung-Bum Shin and Jocelyn F Krey: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Neuroscience, University of Virginia, Charlottesville, Virginia, USA

    Jung-Bum Shin & James M Pagana

  2. Oregon Hearing Research Center, Oregon Health & Science University, Portland, Oregon, USA

    Jung-Bum Shin, Jocelyn F Krey, James M Pagana, Kateri J Spinelli, Hongyu Zhao & Peter G Barr-Gillespie

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

    Ahmed Hassan, Zoltan Metlagel, Andrew N Tauscher & Manfred Auer

  4. W.M. Keck Biomedical Mass Spectrometry Laboratory, University of Virginia, Charlottesville, Virginia, USA

    Nicholas E Sherman & Erin D Jeffery

  5. Department of Biochemistry & Molecular Biology, Oregon Health & Science University, Portland, Oregon, USA

    Phillip A Wilmarth & Larry L David

  6. Department of Public Health & Preventive Medicine, Oregon Health & Science University, Portland, Oregon, USA

    Dongseok Choi

  7. Vollum Institute, Oregon Health & Science University, Portland, Oregon, USA

    Peter G Barr-Gillespie

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Contributions

J.-B.S. and P.G.B.-G. designed the overall approach and analysis. J.F.K. carried out immunoblotting and immunocytochemistry experiments of Figures 2 and 5, as well as Supplementary Figures 2 and 4; she also carried out quantitative immunoblots of Figure 1. J.-B.S. and J.M.P. prepared hair-bundle and epithelium samples for mass spectrometric analysis. A.H., Z.M., A.N.T. and M.A. carried out electron tomography and analyzed tomography data. N.E.S. and E.D.J. carried out mass spectrometry experiments. K.J.S. carried out immunocytochemistry experiments of Supplementary Figure 4. H.Z. carried out immunoprecipitation experiments of Figure 5. D.C. carried out the statistical analyses. P.G.B.-G. carried out mass spectrometry data analysis, with assistance from P.A.W. and L.L.D. The manuscript was written by P.G.B.-G.

Corresponding author

Correspondence to Peter G Barr-Gillespie.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–8 (PDF 12580 kb)

Supplementary Table 1

Chick hair bundle mass spectrometry data (XLS 6442 kb)

Supplementary Table 2

Proteins used to define contaminant fraction (XLS 87 kb)

Supplementary Table 3

Interactions between hair bundle proteins (XLS 68 kb)

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Shin, JB., Krey, J., Hassan, A. et al. Molecular architecture of the chick vestibular hair bundle. Nat Neurosci 16, 365–374 (2013). https://doi.org/10.1038/nn.3312

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