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Patchwork organization of the yeast plasma membrane into numerous coexisting domains

An Addendum to this article was published on 01 August 2012

Abstract

The plasma membrane is made up of lipids and proteins, and serves as an active interface between the cell and its environment. Many plasma-membrane proteins are laterally segregated in the plane of the membrane, but the underlying mechanisms remain controversial. Here we investigate the distribution and dynamics of a representative set of plasma-membrane-associated proteins in yeast cells. These proteins were distributed non-homogeneously in patterns ranging from distinct patches to nearly continuous networks, and these patterns were in turn strongly influenced by the lipid composition of the plasma membrane. Most proteins segregated into distinct domains. However, proteins with similar or identical transmembrane sequences (TMSs) showed a marked tendency to co-localize. Indeed we could predictably relocate proteins by swapping their TMSs. Finally, we found that the domain association of plasma-membrane proteins has an impact on their function. Our results are consistent with self-organization of biological membranes into a patchwork of coexisting domains.

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Figure 1: Test set of plasma-membrane proteins and imaging approach.
Figure 2: Localization patterns of plasma-membrane proteins.
Figure 3: Dynamics of plasma-membrane proteins.
Figure 4: Coexistence of multiple plasma-membrane protein domains.
Figure 5: Real and random overlap value.
Figure 6: Changing localization patterns of plasma-membrane proteins.
Figure 7: Influence of TMSs on protein localization.
Figure 8: Artificial re-targeting of plasma-membrane proteins.

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References

  1. Berchtold, D. & Walther, T. C. TORC2 plasma membrane localization is essential for cell viability and restricted to a distinct domain. Mol. Biol. Cell 20, 1565–1575 (2009).

    Article  CAS  Google Scholar 

  2. Sharma, P. et al. Nanoscale organization of multiple GPI-anchored proteins in living cell membranes. Cell 116, 577–589 (2004).

    Article  CAS  Google Scholar 

  3. Bagatolli, L. A., Ipsen, J. H., Simonsen, A. C. & Mouritsen, O. G. An outlook on organization of lipids in membranes: searching for a realistic connection with the organization of biological membranes. Prog Lipid Res. 49, 378–389 (2010).

    Article  CAS  Google Scholar 

  4. Lingwood, D., Kaiser, H. J., Levental, I. & Simons, K. Lipid rafts as functional heterogeneity in cell membranes. Biochem. Soc. Trans. 37, 955–960 (2009).

    Article  CAS  Google Scholar 

  5. Douglass, A. D. & Vale, R. D. Single-molecule microscopy reveals plasma membrane microdomains created by protein–protein networks that exclude or trap signaling molecules in T cells. Cell 121, 937–950 (2005).

    Article  CAS  Google Scholar 

  6. Kusumi, A., Sako, Y. & Yamamoto, M. Confined lateral diffusion of membrane receptors as studied by single particle tracking (nanovid microscopy). Effects of calcium-induced differentiation in cultured epithelial cells. Biophys. J. 65, 2021–2040 (1993).

    Article  CAS  Google Scholar 

  7. Sackmann, E., Lipowsky, R. & Sackmann, E. Handbook of Biological Physics Vol. 1, Part 1, 1–63 (North-Holland, 1995).

  8. Anderson, R. G. & Jacobson, K. A role for lipid shells in targeting proteins to caveolae, rafts, and other lipid domains. Science 296, 1821–1825 (2002).

    Article  CAS  Google Scholar 

  9. Malı´nská, K., Malı´nská, J., Opekarová, M. & Tanner, W. Visualization of protein compartmentation within the plasma membrane of living yeast cells. Mol. Biol. Cell 14, 4427–4436 (2003).

    Article  Google Scholar 

  10. Kaksonen, M., Toret, C. P. & Drubin, D. G. A modular design for the clathrin- and actin-mediated endocytosis machinery. Cell 123, 305–320 (2005).

    Article  CAS  Google Scholar 

  11. Yu, J. H., Crevenna, A. H., Bettenbuhl, M., Freisinger, T. & Wedlich-Soldner, R. Cortical actin dynamics driven by formins and myosin V. J. Cell Sci. 124, 1533–1541 (2011).

    Article  CAS  Google Scholar 

  12. Walther, T. C. et al. Eisosomes mark static sites of endocytosis. Nature 439, 998–1003 (2006).

    Article  CAS  Google Scholar 

  13. Fiolka, R., Beck, M. & Stemmer, A. Structured illumination in total internal reflection fluorescence microscopy using a spatial light modulator. Opt. Lett. 33, 1629–1631 (2008).

    Article  Google Scholar 

  14. Stauffer, T. P., Ahn, S. & Meyer, T. Receptor-induced transient reduction in plasma membrane PtdIns(4,5)P2 concentration monitored in living cells. Curr. Biol. 8, 343–346 (1998).

    Article  CAS  Google Scholar 

  15. Yeung, T. et al. Membrane phosphatidylserine regulates surface charge and protein localization. Science 319, 210–213 (2008).

    Article  CAS  Google Scholar 

  16. Grossmann, G. et al. Plasma membrane microdomains regulate turnover of transport proteins in yeast. J. Cell Biol. 183, 1075–1088 (2008).

    Article  CAS  Google Scholar 

  17. Ghaemmaghami, S. et al. Global analysis of protein expression in yeast. Nature 425, 737–741 (2003).

    Article  CAS  Google Scholar 

  18. Goswami, D. et al. Nanoclusters of GPI-anchored proteins are formed by cortical actin-driven activity. Cell 135, 1085–1097 (2008).

    Article  CAS  Google Scholar 

  19. Greenberg, M. L. & Axelrod, D. Anomalously slow mobility of fluorescent lipid probes in the plasma membrane of the yeast Saccharomyces cerevisiae. J. Membr. Biol. 131, 115–127 (1993).

    Article  CAS  Google Scholar 

  20. Valdez-Taubas, J. & Pelham, H. R. B. Slow diffusion of proteins in the yeast plasma membrane allows polarity to be maintained by endocytic cycling. Curr. Biol. 13, 1636–1640 (2003).

    Article  CAS  Google Scholar 

  21. Marco, E., Wedlich-Soldner, R., Li, R., Altschuler, S. J. & Wu, L. F. Endocytosis optimizes the dynamic localization of membrane proteins that regulate cortical polarity. Cell 129, 411–422 (2007).

    Article  CAS  Google Scholar 

  22. Manders, E. M. M., Verbeek, F. J. & Aten, J. A. Measurement of co-localization of object in dual-colour confocal images. J. Microsc. 169, 375–382 (1993).

    Article  Google Scholar 

  23. Malinska, K., Malinsky, J., Opekarova, M. & Tanner, W. Distribution of Can1p into stable domains reflects lateral protein segregation within the plasma membrane of living S. cerevisiae cells. J. Cell Sci. 117, 6031–6041 (2004).

    Article  CAS  Google Scholar 

  24. Flegelova, H. & Sychrova, H. Mammalian NHE2 Na(+)/H+ exchanger mediates efflux of potassium upon heterologous expression in yeast. FEBS Lett. 579, 4733–4738 (2005).

    Article  CAS  Google Scholar 

  25. Tarassov, K. et al. An in vivo map of the yeast protein interactome. Science 320, 1465–1470 (2008).

    Article  CAS  Google Scholar 

  26. Momoi, M. et al. SLI1 (YGR212W) is a major gene conferring resistance to the sphingolipid biosynthesis inhibitor ISP-1, and encodes an ISP-1 N-acetyltransferase in yeast. Biochem. J. 381, 321–328 (2004).

    Article  CAS  Google Scholar 

  27. Hikiji, T., Miura, K., Kiyono, K., Shibuya, I. & Ohta, A. Disruption of the CHO1 gene encoding phosphatidylserine synthase in Saccharomyces cerevisiae. J. Biochem. 104, 894–900 (1988).

    Article  CAS  Google Scholar 

  28. Heese-Peck, A. et al. Multiple functions of sterols in yeast endocytosis. Mol. Biol. Cell 13, 2664–2680 (2002).

    Article  CAS  Google Scholar 

  29. Davierwala, A. P. et al. The synthetic genetic interaction spectrum of essential genes. Nat. Genet. 37, 1147–1152 (2005).

    Article  CAS  Google Scholar 

  30. Opekarova, M., Caspari, T. & Tanner, W. Unidirectional arginine transport in reconstituted plasma-membrane vesicles from yeast overexpressing CAN1. Eur. J. Biochem. 211, 683–688 (1993).

    Article  CAS  Google Scholar 

  31. Rothbauer, U. et al. Targeting and tracing antigens in live cells with fluorescent nanobodies. Nat. Methods 3, 887–889 (2006).

    Article  CAS  Google Scholar 

  32. Walther, T. C. et al. Eisosomes mark static sites of endocytosis. Nature 439, 998–1003 (2006).

    Article  CAS  Google Scholar 

  33. Frohlich, F. et al. A genome-wide screen for genes affecting eisosomes reveals Nce102 function in sphingolipid signaling. J. Cell Biol. 185, 1227–1242 (2009).

    Article  Google Scholar 

  34. Engelman, D. M. Membranes are more mosaic than fluid. Nature 438, 578–580 (2005).

    Article  CAS  Google Scholar 

  35. Ejsing, C. S. et al. Global analysis of the yeast lipidome by quantitative shotgun mass spectrometry. Proc. Natl Acad. Sci. USA 106, 2136–2141 (2009).

    Article  CAS  Google Scholar 

  36. Sharpe, H. J., Stevens, T. J. & Munro, S. A comprehensive comparison of transmembrane domains reveals organelle-specific properties. Cell 142, 158–169 (2010).

    Article  CAS  Google Scholar 

  37. Gallego, O. et al. A systematic screen for protein–lipid interactions in Saccharomyces cerevisiae. Mol. Syst. Biol. 6, 430 (2010).

    Article  CAS  Google Scholar 

  38. Hite, R. K., Li, Z. & Walz, T. Principles of membrane protein interactions with annular lipids deduced from aquaporin-0 2D crystals. EMBO J. 29, 1652–1658 (2010).

    Article  CAS  Google Scholar 

  39. Lehtonen, J. Y., Holopainen, J. M. & Kinnunen, P. K. Evidence for the formation of microdomains in liquid crystalline large unilamellar vesicles caused by hydrophobic mismatch of the constituent phospholipids. Biophys. J. 70, 1753–1760 (1996).

    Article  CAS  Google Scholar 

  40. Thomas, C. L., Bayer, E. M., Ritzenthaler, C., Fernandez-Calvino, L. & Maule, A. J. Specific targeting of a plasmodesmal protein affecting cell-to-cell communication. PLoS Biol. 6, e7 (2008).

    Article  Google Scholar 

  41. Day, C. A. & Kenworthy, A. K. Tracking microdomain dynamics in cell membranes. Biochim. Biophys. Acta 1788, 245–253 (2009).

    Article  CAS  Google Scholar 

  42. Fan, J., Sammalkorpi, M. & Haataja, M. Formation and regulation of lipid microdomains in cell membranes: theory, modeling, and speculation. FEBS Lett. 584, 1678–1684 (2010).

    Article  CAS  Google Scholar 

  43. Bagnat, M. & Simons, K. Cell surface polarization during yeast mating. Proc. Natl Acad. Sci. USA 99, 14183–14188 (2002).

    Article  CAS  Google Scholar 

  44. Tyteca, D. et al. Three unrelated sphingomyelin analogs spontaneously cluster into plasma membrane micrometric domains. Biochim. Biophys. Acta 1798, 909–927 (2010).

    Article  CAS  Google Scholar 

  45. Lauwers, E. & André, B. Association of yeast transporters with detergent-resistant membranes correlates with their cell-surface location. Traffic 7, 1045–1059 (2006).

    Article  CAS  Google Scholar 

  46. Opekarova, M., Malinska, K., Novakova, L. & Tanner, W. Differential effect of phosphatidylethanolamine depletion on raft proteins: further evidence for diversity of rafts in Saccharomyces cerevisiae. Biochim. Biophys. Acta 1711, 87–95 (2005).

    Article  CAS  Google Scholar 

  47. Janke, C. et al. A versatile toolbox for PCR-based tagging of yeast genes: new fluorescent proteins, more markers and promoter substitution cassettes. Yeast 21, 947–962 (2004).

    Article  CAS  Google Scholar 

  48. Huh, W-K. et al. Global analysis of protein localization in budding yeast. Nature 425, 686–691 (2003).

    Article  CAS  Google Scholar 

  49. George, N., Pick, H., Vogel, H., Johnsson, N. & Johnsson, K. Specific labeling of cell surface proteins with chemically diverse compounds. J. Am. Chem. Soc. 126, 8896–8897 (2004).

    Article  CAS  Google Scholar 

  50. Hirvonen, L. M., Wicker, K., Mandula, O. & Heintzmann, R. Structured illumination microscopy of a living cell. Eur. Biophys. J. 38, 807–812 (2009).

    Article  Google Scholar 

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Acknowledgements

We are indebted to A. Rohrbach for providing access to the TIRF-SIM microscope and analysis. We thank N. Johnsson (Institute for Molecular Genetics and Cell Biology, Ulm University, Germany) for providing the plasmid ACP–Sag1 and P. Hardy for editorial assistance. This work was financially supported by the Max Planck Society.

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R.W-S., F.S. and N.S.M. designed all experiments. F.S. performed all microscopy and experiments with help from G.B. N.S.M., F.S., J.B. and R.W-S. analysed the data. P.v.O. and F.S. performed the TIRF-SIM experiments. F.S., N.S.M. and R.W-S. wrote the paper.

Corresponding author

Correspondence to Roland Wedlich-Söldner.

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The authors declare no competing financial interests.

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Spira, F., Mueller, N., Beck, G. et al. Patchwork organization of the yeast plasma membrane into numerous coexisting domains. Nat Cell Biol 14, 640–648 (2012). https://doi.org/10.1038/ncb2487

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