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A plasma-membrane E-MAP reveals links of the eisosome with sphingolipid metabolism and endosomal trafficking

Nature Structural & Molecular Biology volume 17, pages 901–908 (2010)Cite this article

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Abstract

The plasma membrane delimits the cell and controls material and information exchange between itself and the environment. How different plasma-membrane processes are coordinated and how the relative abundance of plasma-membrane lipids and proteins is homeostatically maintained are not yet understood. Here, we used a quantitative genetic interaction map, or E-MAP, to functionally interrogate a set of ∼400 genes involved in various aspects of plasma-membrane biology, including endocytosis, signaling, lipid metabolism and eisosome function. From this E-MAP, we derived a set of 57,799 individual interactions between genes functioning in these various processes. Using triplet genetic motif analysis, we identified a new component of the eisosome, Eis1, and linked the poorly characterized gene EMP70 to endocytic and eisosome function. Finally, we implicated Rom2, a GDP/GTP exchange factor for Rho1 and Rho2, in the regulation of sphingolipid metabolism.

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Figure 1: Composition of the plasma membrane E-MAP.
Figure 2: Overview of the clustergram of the plasma membrane E-MAP.
Figure 3: TGMs of the plasma membrane E-MAP.
Figure 4: YMR031C/EIS1 encodes an eisosome component.
Figure 5: The eisosome-linked Emp70 is an early endosomal protein.
Figure 6: Emp70 is required for normal endosome function.
Figure 7: Genetic interactions of sphingolipid metabolism.
Figure 8: Rom2 interacts with sphingolipid metabolism.

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Acknowledgements

We thank members of the Walther and Krogan laboratory for critical reading and comments, J. Brickner for suggestions, Ulrike Laabs for excellent technical assistance, O. Nørregaard Jensen (University of Southern Denmark) for providing access to the Nanomate Triversa used for the lipidomic experiments and P. Kemmeren for establishing the database. This work was supported by the Max Planck Society (T.C.W.), the German Research Foundation (DFG; T.C.W.), the German-Israeli Foundation (T.C.W.), the US National Institutes of Health, the Searle, Sandler and Keck Foundations (N.J.K.), the International Human Frontier Science Program (HFSP; T.C.W.), the Israel Science Foundation (grant no. 802/08; R.S.), the Edmond J. Safra Bioinformatics program at Tel Aviv University (I.U.), the Programa de Apoyo Sectorial a la Estrategia Nacional de Innovación (INNOVA URUGUAY, DCI-ALA/2007/19.040, P.S.A.), the Agencia Nacional de Investigación e Innovación (ANII, A.O.-C.), the Danish Council for Independent Research (DOK1155860, C.S.E.) and Lundbeckfonden (R45-A4342, C.S.E.).

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Author notes

  1. Igor Ulitsky

    Present address: Present address: Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA.,

  2. Pablo S Aguilar, Florian Fröhlich, Michael Rehman and Mike Shales: These authors contributed equally to this work.

Authors and Affiliations

  1. Institut Pasteur de Montevideo, Montevideo, Uruguay

    Pablo S Aguilar & Agustina Olivera-Couto

  2. Max Planck Institute of Biochemistry, Organelle Architecture and Dynamics, Martinsried, Germany

    Florian Fröhlich, Michael Rehman & Tobias C Walther

  3. Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA

    Mike Shales, Hannes Braberg & Nevan J Krogan

  4. The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel

    Igor Ulitsky & Ron Shamir

  5. Department of Biochemistry and Biophysics, University of California and Howard Hughes Medical Institute, San Francisco, California, USA

    Peter Walter

  6. Max Planck Institute of Biochemistry, Proteomics and Signal Transduction, Martinsried, Germany

    Matthias Mann

  7. Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark

    Christer S Ejsing

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All authors contributed to every aspect of this work.

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Correspondence to Nevan J Krogan or Tobias C Walther.

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Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–5, Supplementary Tables 3–7 (PDF 10198 kb)

Supplementary Table 1

Classification of genes used for Figure 1a (XLS 67 kb)

Supplementary Table 2

Correlations of genes pairs in the plasma membrane E-MAP used in Figures 1b and 1c. (XLS 12860 kb)

Supplementary Video 1

Localization of Emp70-GFP. (AVI 11923 kb)

Supplementary Video 2

Localization of Emp70-GFP in respect to Lsp1-RFPmars. (AVI 11887 kb)

Supplementary Data

Treeview representation for clustergram of the PM E-MAP, composed of 4 files (.atr, .cdt,.gtr.,jtv). These files can be opened by a treeview program such as Java Treeview that can be found at: http://jtreeview.sourceforge.net/. (ZIP 471 kb)

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Aguilar, P., Fröhlich, F., Rehman, M. et al. A plasma-membrane E-MAP reveals links of the eisosome with sphingolipid metabolism and endosomal trafficking. Nat Struct Mol Biol 17, 901–908 (2010). https://doi.org/10.1038/nsmb.1829

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