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Mapping the functional yeast ABC transporter interactome

Nature Chemical Biology volume 9, pages 565–572 (2013)Cite this article

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Abstract

ATP-binding cassette (ABC) transporters are a ubiquitous class of integral membrane proteins of immense clinical interest because of their strong association with human disease and pharmacology. To improve our understanding of these proteins, we used membrane yeast two-hybrid technology to map the protein interactome of all of the nonmitochondrial ABC transporters in the model organism Saccharomyces cerevisiae and combined this data with previously reported yeast ABC transporter interactions in the BioGRID database to generate a comprehensive, integrated 'interactome'. We show that ABC transporters physically associate with proteins involved in an unexpectedly diverse range of functions. We specifically examine the importance of the physical interactions of ABC transporters in both the regulation of one another and in the modulation of proteins involved in zinc homeostasis. The interaction network presented here will be a powerful resource for increasing our fundamental understanding of the cellular role and regulation of ABC transporters.

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Figure 1: Overview of ABC transporters in Saccharomyces cerevisiae and validation of MYTH-tagged baits.
Figure 2: Integrated ABC transporter interactome.
Figure 3: Investigation of interactions between full-size ABC transporters.
Figure 4: Investigating role of ABC transporters in zinc homeostasis.

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Acknowledgements

This work is dedicated to our late friend and colleague Igor Shevelev. We thank B. Andrews, C. Nislow, F. Vizeacoumar, C. Kurat and S. Alfred (University of Toronto) for providing reagents, assistance and equipment; L. Miller, S. Pagant, K. Kuchler and C. Klein for experimental assistance; and W.K. Huh (Seoul National University) for providing BiFC plasmids. We also thank V. Kanelis, K. Sokolina and M. Ali for reviewing the manuscript. This work was supported by grants from the Canadian Institutes of Health Research, Canadian Foundation for Innovation, Natural Sciences and Engineering Research Council of Canada, Ontario Genomics Institute, Canadian Cystic Fibrosis Foundation, Canadian Cancer Society, University Health Network to I. Stagljar and National Institutes of Health (R01-GM76375 to H.-O.P. and R01-GM51508 to S.M.).

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Authors and Affiliations

  1. Donnelly Centre, University of Toronto, Toronto, Ontario, Canada

    Jamie Snider, Asad Hanif, Ke Jin, Analyn R Yu, Chris Graham, Matthew Chuk, Dunja Damjanovic, Marta Wierzbicka, Priscilla Tang, Victoria Wong, Katelyn D Darowski, Bryan-Joseph San Luis, Igor Shevelev, Charles Boone, Jack F Greenblatt, Zhaolei Zhang & Igor Stagljar

  2. Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada

    Asad Hanif, Ke Jin, Matthew Chuk, Dunja Damjanovic, Priscilla Tang, Bryan-Joseph San Luis, Charles Boone, Jack F Greenblatt, Zhaolei Zhang & Igor Stagljar

  3. Molecular Cellular Developmental Biology Program, The Ohio State University, Columbus, Ohio, USA

    Mid Eum Lee & Hay-Oak Park

  4. Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada

    Ke Jin, Bryan-Joseph San Luis, Charles Boone, Jack F Greenblatt & Zhaolei Zhang

  5. Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, Saskatchewan, Canada

    Chris Graham, Matthew Jessulat & Mohan Babu

  6. Department of Pediatrics, Columbia University Medical Center, New York, New York, USA

    Dina Balderes & Stephen L Sturley

  7. Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada

    Katelyn D Darowski & Igor Stagljar

  8. Graduate Center for Toxicology, University of Kentucky, Lexington, Kentucky, USA

    Christian M Paumi

  9. Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, USA

    Hay-Oak Park

  10. Department of Cell Biology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA

    Susan Michaelis

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  1. Jamie Snider
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Contributions

I. Stagljar designed the project. J.S. was actively involved in all experiments, and wrote the bulk of the manuscript. I. Stagljar and S.M. provided project guidance and assisted in manuscript preparation. K.J. and Z.Z. performed bioinformatics analysis. H.-O.P. and M.E.L. performed BiFC experiments. A.R.Y. performed Westerns, phenotype assays and strain generation. A.H. carried out MYTH screening and zinc-related functional analysis. M.C., D.D., C.G., M.W., P.T. and V.W. carried out MYTH screening. S.L.S. and D.B. carried out MYTH screening of AUS1 under anaerobic conditions. K.D.D. carried out the PDR11 and AUS1 western blots. C.G., M.J., J.F.G and M.B. performed co-IP experiments. C.B. and B.-J.S.L. provided deletion strains. C.M.P. carried out zinc transport assays. H.-O.P. and C.M.P. critically reviewed the manuscript. I. Shevelev was involved in bait strain generation and initial project design.

Corresponding author

Correspondence to Igor Stagljar.

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Competing interests

I. Stagljar is cofounder of Dualsystems Biotech, Switzerland.

Supplementary information

Supplementary Text and Figures

Supplementary Results, Supplementary Figures 1–25 and Supplementary Tables 1–2 (PDF 5999 kb)

Supplementary Data Set 1

Comprehensive list of all hits identified in MYTH screening. (XLSX 16 kb)

Supplementary Data Set 2

Comprehensive list of all members of the integrated ABC transporter interactome annotated to identify those with human orthologs and human orthologs associated with (XLSX 34 kb)

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Snider, J., Hanif, A., Lee, M. et al. Mapping the functional yeast ABC transporter interactome. Nat Chem Biol 9, 565–572 (2013). https://doi.org/10.1038/nchembio.1293

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