Systematic multi-level analysis of an organelle proteome reveals new peroxisomal functions

Yifrach, E.; Holbrook-Smith, D.; Bürgi, J.; Othman, A.; Eisenstein, M.; Van Roermund, C. W. T.; Visser, W.; Tirosh, A.; Bibi, C.; Galor, S.; Weil, U.; Fadel, A.; Peleg, Y.; Waterham, H.; Wanders, R. J.; Wilmanns, M.; Zamboni, N.; Schuldiner, M.; Zalckvar, E.

doi:10.1101/2021.12.08.471723

bioRxiv · 10.1101/2021.12.08.471723

Systematic multi-level analysis of an organelle proteome reveals new peroxisomal functions

Yifrach, E.·Holbrook-Smith, D.·Bürgi, J.·Othman, A.·Eisenstein, M.·Van Roermund, C. W. T.·Visser, W.·Tirosh, A.·Bibi, C.·Galor, S.·Weil, U.·Fadel, A.·Peleg, Y.·Waterham, H.·Wanders, R. J.·Wilmanns, M.·Zamboni, N.·Schuldiner, M.·Zalckvar, E.

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Abstract

Seventy years following the discovery of peroxisomes, their proteome remains undefined. Uncovering the complete peroxisomal proteome, the peroxi-ome, is crucial for understanding peroxisomal activities and cellular metabolism. We used high-content microscopy to uncover the peroxi-ome of the model eukaryote - Saccharomyces cerevisiae. This strategy enabled us to expand the known organellar proteome by [~]40% and paved the way for performing systematic, whole-organellar proteome assays. Coupled with targeted experiments this allowed us to discover new peroxisomal functions. By characterizing the sub-organellar localization and protein targeting dependencies into the organelle, we unveiled non-canonical targeting routes. Metabolomic analysis of the peroxi-ome revealed the role of several newly-identified resident enzymes. Importantly, we found a regulatory role of peroxisomes during gluconeogenesis, which is fundamental for understanding cellular metabolism. With the current recognition that peroxisomes play a crucial part in organismal physiology, our approach lays the foundation for deep characterization of peroxisome function in health and disease.

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Yifrach, E., Holbrook-Smith, D., Bürgi, J., Othman, A., Eisenstein, M., Van Roermund, C. W. T., Visser, W., Tirosh, A., Bibi, C., Galor, S., Weil, U., Fadel, A., Peleg, Y., Waterham, H., Wanders, R. J., Wilmanns, M., Zamboni, N., Schuldiner, M., Zalckvar, E.. 2021-12-11. Systematic multi-level analysis of an organelle proteome reveals new peroxisomal functions. https://doi.org/10.1101/2021.12.08.471723

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