Genome-wide SWAp-Tag yeast libraries for proteome exploration

Uri Weill; Ido Yofe; Ehud Sass; Bram Stynen; Dan Davidi; Janani Natarajan; Reut Ben-Menachem; Zohar Avihou; Omer Goldman; Nofar Harpaz; Silvia Chuartzman; Kiril Kniazev; Barbara Knoblach; Janina Laborenz; Felix Boos; Jacqueline Kowarzyk; Shifra Ben-Dor; Einat Zalckvar; Johannes M. Herrmann; Richard A. Rachubinski; Ophry Pines; Doron Rapaport; Stephen W. Michnick; Emmanuel D. Levy; Maya Schuldiner

doi:10.1038/s41592-018-0044-9

Genome-wide SWAp-Tag yeast libraries for proteome exploration

Uri Weill, Ido Yofe, Ehud Sass, Bram Stynen, Dan Davidi, Janani Natarajan, Reut Ben-Menachem, Zohar Avihou, Omer Goldman, Nofar Harpaz, Silvia Chuartzman, Kiril Kniazev, Barbara Knoblach, Janina Laborenz, Felix Boos, Jacqueline Kowarzyk, Shifra Ben-Dor, Einat Zalckvar, Johannes M. Herrmann, Richard A. RachubinskiOphry Pines, Doron Rapaport, Stephen W. Michnick, Emmanuel D. Levy, Maya Schuldiner^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

105 Scopus citations

Abstract

Yeast libraries revolutionized the systematic study of cell biology. To extensively increase the number of such libraries, we used our previously devised SWAp-Tag (SWAT) approach to construct a genome-wide library of ~5,500 strains carrying the SWAT NOP1promoter-GFP module at the N terminus of proteins. In addition, we created six diverse libraries that restored the native regulation, created an overexpression library with a Cherry tag, or enabled protein complementation assays from two fragments of an enzyme or fluorophore. We developed methods utilizing these SWAT collections to systematically characterize the yeast proteome for protein abundance, localization, topology, and interactions.

Original language	English
Pages (from-to)	617-622
Number of pages	6
Journal	Nature Methods
Volume	15
Issue number	8
DOIs	https://doi.org/10.1038/s41592-018-0044-9
State	Published - 1 Aug 2018

Bibliographical note

Funding Information:
We thank Y. Peleg for plasmid construction, G. Brodsky for graphics, R. Rotkopf for support in statistical analysis, K. Tedrick for technical help with the Y2H experiments, and C. Meisinger and N. Vögtle for help with the MTS assignments. We thank G. Krieger for helpful discussions and technical help. We thank C. Ungermann (University of Osnabrück, Germany) and W.-K. Huh (Seoul National University, Seoul, South Korea) for plasmids. The work in the Schuldiner laboratory was supported by ERC CoG Peroxisystem (646604), SFB 1190 from the DFG, a Mitzutani foundation grant, and a VolksWagen foundation grant (93092). The collaborative work on this manuscript done by the Schuldiner, Pines, Herrmann, and Rapaport laboratories was supported by a DIP grant (P17516). Work at the Rachubinski lab was supported by Foundation Grant FDN-143289 from the Canadian Institutes of Health Research. Work in the Michnick lab was supported by Canadian Institutes of Health Research grant MOP-GMX-152556. Work in the Levy lab was supported by Israel Science Foundation grants 1775/12 and 2179/14. U.W. and D.D. are recipients of the Azrieli student-award grant. M.S. is an Incumbent of the Dr. Gilbert Omenn and Martha Darling Professorial Chair in Molecular Genetics.

Publisher Copyright:
© 2018, The Author(s).

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Weill, U., Yofe, I., Sass, E., Stynen, B., Davidi, D., Natarajan, J., Ben-Menachem, R., Avihou, Z., Goldman, O., Harpaz, N., Chuartzman, S., Kniazev, K., Knoblach, B., Laborenz, J., Boos, F., Kowarzyk, J., Ben-Dor, S., Zalckvar, E., Herrmann, J. M., ... Schuldiner, M. (2018). Genome-wide SWAp-Tag yeast libraries for proteome exploration. Nature Methods, 15(8), 617-622. https://doi.org/10.1038/s41592-018-0044-9

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abstract = "Yeast libraries revolutionized the systematic study of cell biology. To extensively increase the number of such libraries, we used our previously devised SWAp-Tag (SWAT) approach to construct a genome-wide library of ~5,500 strains carrying the SWAT NOP1promoter-GFP module at the N terminus of proteins. In addition, we created six diverse libraries that restored the native regulation, created an overexpression library with a Cherry tag, or enabled protein complementation assays from two fragments of an enzyme or fluorophore. We developed methods utilizing these SWAT collections to systematically characterize the yeast proteome for protein abundance, localization, topology, and interactions.",

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Weill, U, Yofe, I, Sass, E, Stynen, B, Davidi, D, Natarajan, J, Ben-Menachem, R, Avihou, Z, Goldman, O, Harpaz, N, Chuartzman, S, Kniazev, K, Knoblach, B, Laborenz, J, Boos, F, Kowarzyk, J, Ben-Dor, S, Zalckvar, E, Herrmann, JM, Rachubinski, RA, Pines, O, Rapaport, D, Michnick, SW, Levy, ED & Schuldiner, M 2018, 'Genome-wide SWAp-Tag yeast libraries for proteome exploration', Nature Methods, vol. 15, no. 8, pp. 617-622. https://doi.org/10.1038/s41592-018-0044-9

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AU - Yofe, Ido

AU - Sass, Ehud

AU - Stynen, Bram

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AU - Natarajan, Janani

AU - Ben-Menachem, Reut

AU - Avihou, Zohar

AU - Goldman, Omer

AU - Harpaz, Nofar

AU - Chuartzman, Silvia

AU - Kniazev, Kiril

AU - Knoblach, Barbara

AU - Laborenz, Janina

AU - Boos, Felix

AU - Kowarzyk, Jacqueline

AU - Ben-Dor, Shifra

AU - Zalckvar, Einat

AU - Herrmann, Johannes M.

AU - Rachubinski, Richard A.

AU - Pines, Ophry

AU - Rapaport, Doron

AU - Michnick, Stephen W.

AU - Levy, Emmanuel D.

AU - Schuldiner, Maya

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Genome-wide SWAp-Tag yeast libraries for proteome exploration

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