Abstract

Mitochondrial dysfunction is associated with many human diseases, including cancer and neurodegeneration, that are often linked to proteins and pathways that are not well-characterized. To begin defining the functions of such poorly characterized proteins, we used mass spectrometry to map the proteomes, lipidomes, and metabolomes of 174 yeast strains, each lacking a single gene related to mitochondrial biology. 144 of these genes have human homologs, 60 of which are associated with disease and 39 of which are uncharacterized. We present a multi-omic data analysis and visualization tool that we use to find covariance networks that can predict molecular functions, correlations between profiles of related gene deletions, gene-specific perturbations that reflect protein functions, and a global respiration deficiency response. Using this multi-omic approach, we link seven proteins including Hfd1p and its human homolog ALDH3A1 to mitochondrial coenzyme Q (CoQ) biosynthesis, an essential pathway disrupted in many human diseases. This Resource should provide molecular insights into mitochondrial protein functions.

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Acknowledgements

We thank members of the Pagliarini and Coon laboratories for helpful discussions. This work was supported by a Searle Scholars Award and NIH grants R01DK098672, R01GM112057, and R01GM115591 (to D.J.P.); NIH grant R35GM118110 (to J.J.C.); NIH Ruth L. Kirschstein NRSA F30AG043282 (to J.A.S.); DOE Great Lakes Bioenergy Research Center (DOE Office of Science BER DE-FC02-07ER64494 to N.W.K. and A.U.); and ACS Analytical Chemistry and Society of Analytical Chemists of Pittsburgh awards (to A.L.R.); NSF Graduate Research Fellowship and NIH T32GM007215 (to M.T.V.); NIH T32DK007665 (to Z.A.K.); and NIH T32HG002760 (to E.A.T.).

Author information

Author notes

    • Jonathan A Stefely
    •  & Nicholas W Kwiecien

    These authors contributed equally to this work.

    • David J Pagliarini
    •  & Joshua J Coon

    These authors jointly supervised this work.

Affiliations

  1. Morgridge Institute for Research, Madison, Wisconsin, USA.

    • Jonathan A Stefely
    • , Adam Jochem
    • , Kyle P Robinson
    • , Mike T Veling
    • , Xiao Guo
    • , Zachary A Kemmerer
    • , Jacob Sokol
    •  & David J Pagliarini
  2. Department of Biochemistry, University of Wisconsin–Madison, Madison, Wisconsin, USA.

    • Jonathan A Stefely
    • , Kyle P Robinson
    • , Mike T Veling
    • , Zachary A Kemmerer
    • , Jacob Sokol
    •  & David J Pagliarini
  3. Genome Center of Wisconsin, Madison, Wisconsin, USA.

    • Nicholas W Kwiecien
    • , Elyse C Freiberger
    • , Alicia L Richards
    • , Matthew J P Rush
    • , Arne Ulbrich
    • , Paul D Hutchins
    • , Kyle J Connors
    • , Edna A Trujillo
    • , Harald Marx
    • , Michael S Westphall
    • , Alexander S Hebert
    •  & Joshua J Coon
  4. Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin, USA.

    • Nicholas W Kwiecien
    • , Alicia L Richards
    • , Matthew J P Rush
    • , Arne Ulbrich
    • , Paul D Hutchins
    • , Xiao Guo
    • , Kyle J Connors
    • , Edna A Trujillo
    •  & Joshua J Coon
  5. Department of Biomolecular Chemistry, University of Wisconsin–Madison, Madison, Wisconsin, USA.

    • Elyse C Freiberger
    •  & Joshua J Coon

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Contributions

J.A.S., N.W.K., D.J.P., and J.J.C. conceived of the project and its design and wrote the manuscript. J.A.S., A.J., K.P.R., X.G., Z.A.K., and J.S. prepared samples and performed biochemical experiments. E.C.F., A.L.R., M.J.P.R., A.U., P.D.H., X.G., K.J.C., E.A.T., and A.S.H. acquired MS data. J.A.S., N.W.K., M.T.V., H.M., M.S.W., D.J.P., and J.J.C. analyzed data.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to David J Pagliarini or Joshua J Coon.

Integrated supplementary information

Supplementary information

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  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–14 and Supplementary Notes 1–7

Excel files

  1. 1.

    Supplementary Table 1

    Knockout yeast strains.

  2. 2.

    Supplementary Table 2

    Profiled biomolecules

  3. 3.

    Supplementary Table 3

    Quantitative dataset

  4. 4.

    Supplementary Table 4

    gene-specific phenotypes.

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    Supplementary Table 5

    Respiration deficient strains vs respiration competent strains.

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    Supplementary Table 6

    Respiration deficient strains versus wild type.

  7. 7.

    Supplementary Table 7

    gene-Δgene perturbation profile correlations.

  8. 8.

    Supplementary Table 8

    Molecule covariance network analysis results

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    Supplementary Code

    Source Code

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DOI

https://doi.org/10.1038/nbt.3683

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