Charting organellar importomes by quantitative mass spectrometry

Christian D. Peikert, Jan Mani, Marcel Morgenstern, Sandro Käser, Bettina Knapp, Christoph Wenger, Anke Harsman, Silke Oeljeklaus, André Schneider () and Bettina Warscheid ()
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Christian D. Peikert: Faculty of Biology, Institute of Biology II, University of Freiburg
Jan Mani: University of Bern
Marcel Morgenstern: Faculty of Biology, Institute of Biology II, University of Freiburg
Sandro Käser: University of Bern
Bettina Knapp: Faculty of Biology, Institute of Biology II, University of Freiburg
Christoph Wenger: University of Bern
Anke Harsman: University of Bern
Silke Oeljeklaus: Faculty of Biology, Institute of Biology II, University of Freiburg
André Schneider: University of Bern
Bettina Warscheid: Faculty of Biology, Institute of Biology II, University of Freiburg

Nature Communications, 2017, vol. 8, issue 1, 1-14

Abstract: Abstract Protein import into organelles is essential for all eukaryotes and facilitated by multi-protein translocation machineries. Analysing whether a protein is transported into an organelle is largely restricted to single constituents. This renders knowledge about imported proteins incomplete, limiting our understanding of organellar biogenesis and function. Here we introduce a method that enables charting an organelle’s importome. The approach relies on inducible RNAi-mediated knockdown of an essential subunit of a translocase to impair import and quantitative mass spectrometry. To highlight its potential, we established the mitochondrial importome of Trypanosoma brucei, comprising 1,120 proteins including 331 new candidates. Furthermore, the method allows for the identification of proteins with dual or multiple locations and the substrates of distinct protein import pathways. We demonstrate the specificity and versatility of this ImportOmics method by targeting import factors in mitochondria and glycosomes, which demonstrates its potential for globally studying protein import and inventories of organelles.

Date: 2017
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DOI: 10.1038/ncomms15272

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