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Mol Syst Biol. 2010; 6: 430.
Published online Nov 30, 2010. doi:  10.1038/msb.2010.87
PMCID: PMC3010107
A systematic screen for protein–lipid interactions in Saccharomyces cerevisiae
Oriol Gallego,1 Matthew J Betts,1* Jelena Gvozdenovic-Jeremic,1 Kenji Maeda,1 Christian Matetzki,1 Carmen Aguilar-Gurrieri,1 Pedro Beltran-Alvarez,1 Stefan Bonn,1 Carlos Fernández-Tornero,1 Lars Juhl Jensen,1 Michael Kuhn,1§ Jamie Trott,1 Vladimir Rybin,2 Christoph W Müller,1 Peer Bork,1 Marko Kaksonen,3 Robert B Russell,1* and Anne-Claude Gavina1
1Structural and Computational Biology Unit, European Molecular Biology Laboratory, EMBL, Heidelberg, Germany
2Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, EMBL, Heidelberg, Germany
3Protein Expression and Purification Core Facility, European Molecular Biology Laboratory, EMBL, Heidelberg, Germany
aStructural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany. Tel.: +49 622 138 78816; Fax: +49 622 138 7519; gavin/at/
*Present address: Cell Networks, University of Heidelberg, 69120 Heidelberg, Germany
Present address: Centro de Investigaciones Biológicas-CSIC, 28040 Madrid, Spain
Present address: Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark
§Present address: Biotec, TU Dresden, 01062 Dresden, Germany
Received June 16, 2010; Accepted October 4, 2010.
Protein–metabolite networks are central to biological systems, but are incompletely understood. Here, we report a screen to catalog protein–lipid interactions in yeast. We used arrays of 56 metabolites to measure lipid-binding fingerprints of 172 proteins, including 91 with predicted lipid-binding domains. We identified 530 protein–lipid associations, the majority of which are novel. To show the data set's biological value, we studied further several novel interactions with sphingolipids, a class of conserved bioactive lipids with an elusive mode of action. Integration of live-cell imaging suggests new cellular targets for these molecules, including several with pleckstrin homology (PH) domains. Validated interactions with Slm1, a regulator of actin polarization, show that PH domains can have unexpected lipid-binding specificities and can act as coincidence sensors for both phosphatidylinositol phosphates and phosphorylated sphingolipids.
Keywords: interactome, lipid–array, network, pleckstrin homology domains, sphingolipids
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