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Interaction landscape of membrane-protein complexes in Saccharomyces cerevisiae

Abstract

Macromolecular assemblies involving membrane proteins (MPs) serve vital biological roles and are prime drug targets in a variety of diseases1. Large-scale affinity purification studies of soluble-protein complexes have been accomplished for diverse model organisms, but no global characterization of MP-complex membership has been described so far. Here we report a complete survey of 1,590 putative integral, peripheral and lipid-anchored MPs from Saccharomyces cerevisiae, which were affinity purified in the presence of non-denaturing detergents. The identities of the co-purifying proteins were determined by tandem mass spectrometry and subsequently used to derive a high-confidence physical interaction map encompassing 1,726 membrane protein–protein interactions and 501 putative heteromeric complexes associated with the various cellular membrane systems. Our analysis reveals unexpected physical associations underlying the membrane biology of eukaryotes and delineates the global topological landscape of the membrane interactome.

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Figure 1: Proteome- wide purification of yeast MPs.
Figure 2: Global organization of yeast MP complexes.
Figure 3: Functional association of Irc6 with AP1.
Figure 4: Ssp120 participates in Golgi to ER recycling.

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Acknowledgements

We thank H. Riezman, K. Sato and A. Nakano for providing strains and reagents, C. Ungermann for Sec18 antisera, A. Pierleoni for assistance with MemPype and R. Zheng for technical assistance. This research was supported by grants from the Canadian Foundation for Innovation, the Canadian Institutes of Health Research (CIHR MOP no. 81156, MOP no. 64394 and MOP no. 82940), the Canadian Cancer Society Research Institute, the Heart and Stroke Foundation, the Cystic Fibrosis Foundation, Novartis, the Ontario Genomics Institute and Genome Canada. E.C. is a CIHR New Investigator. S.J.W. is a Canada Research Chair Tier-I and acknowledges support from the SickKids Foundation.

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J.F.G., A.E. and M.B. designed the project. M.B. coordinated and managed all experiments, and data analysis was coordinated by J.V. with guidance from S.J.W. and M.B. X.G., O.H., G.Z. and J.L. prepared the purification samples. S.C., N.B. and C.C. carried out mass spectrometry. V.F., T.P. and S.P. (CCBR) performed database searches and curation. J.V. and S.P. (CCBR) designed the web portal. J.V., M.B. and S.P. (SickKids) analysed the network data. M.B., C.G., B.D.M.B., J.S., V.W., A.Y., Y.Y.C.T., H.E.B., M.D. and F.J.V. carried out validation experiments. M.B., J.V., E.C., S.J.W. and A.E. jointly drafted the manuscript with critical input from J.F.G., and contributions from I.S., J.S. and B.D.M.B. All authors discussed the results and commented on the manuscript.

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Correspondence to Elizabeth Conibear, Shoshana J. Wodak, Andrew Emili or Jack F. Greenblatt.

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The authors declare no competing financial interests.

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This file contains Supplementary Text and Data, Supplementary References, legends for Supplementary Tables 1-13 (see separate zipped file) and Supplementary Figures 1-7. (PDF 1327 kb)

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Babu, M., Vlasblom, J., Pu, S. et al. Interaction landscape of membrane-protein complexes in Saccharomyces cerevisiae. Nature 489, 585–589 (2012). https://doi.org/10.1038/nature11354

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