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Cross-linking of the Endolysosomal System Reveals Flotillin Structures and Putative Cargo

Jasjot Singh, Hadeer Elhabashy, Pathma Muthukottiappan, Markus Stepath, Martin Eisenacher, Oliver Kohlbacher, Volkmar Gieselmann, Dominic Winter
doi: https://doi.org/10.1101/2022.01.12.475930
Jasjot Singh
1Institute for Biochemistry and Molecular Biology, Medical Faculty, University of Bonn, 53115 Bonn, Germany.
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  • For correspondence: jsin@uni-bonn.de dominic.winter@uni-bonn.de
Hadeer Elhabashy
2Department of Protein Evolution, Max-Planck-Institute for Developmental Biology, Max-Planck- Ring 5, 72076 Tübingen, Germany.
3Institute for Bioinformatics and Medical Informatics, University of Tübingen, Sand 14, 72076, Tübingen, Germany.
4Department of Computer Science, University of Tübingen, Sand 14, 72076 Tübingen, Germany.
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Pathma Muthukottiappan
1Institute for Biochemistry and Molecular Biology, Medical Faculty, University of Bonn, 53115 Bonn, Germany.
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Markus Stepath
5Medizinisches Proteom-Center, Medical Faculty, Ruhr-University Bochum, Bochum, Germany.
6Medical Proteome Analysis, Center for Protein Diagnostics, Ruhr-University Bochum, Bochum, Germany.
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Martin Eisenacher
5Medizinisches Proteom-Center, Medical Faculty, Ruhr-University Bochum, Bochum, Germany.
6Medical Proteome Analysis, Center for Protein Diagnostics, Ruhr-University Bochum, Bochum, Germany.
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Oliver Kohlbacher
3Institute for Bioinformatics and Medical Informatics, University of Tübingen, Sand 14, 72076, Tübingen, Germany.
4Department of Computer Science, University of Tübingen, Sand 14, 72076 Tübingen, Germany.
7Institute for Translational Bioinformatics, University Hospital Tübingen, 72076 Tübingen, Germany.
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Volkmar Gieselmann
1Institute for Biochemistry and Molecular Biology, Medical Faculty, University of Bonn, 53115 Bonn, Germany.
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Dominic Winter
1Institute for Biochemistry and Molecular Biology, Medical Faculty, University of Bonn, 53115 Bonn, Germany.
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  • For correspondence: jsin@uni-bonn.de dominic.winter@uni-bonn.de
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SUMMARY

Lysosomes are well-established as the main cellular organelles for the degradation of macromolecules and emerging as regulatory centers of metabolism. They are of crucial importance for cellular homeostasis, which is exemplified by a plethora of disorders related to alterations in lysosomal function. In this context, protein complexes play a decisive role, regulating not only metabolic lysosomal processes, but also lysosome biogenesis, transport, and interaction with other organelles. Using cross-linking mass spectrometry, we analyzed lysosomes and early endosomes. Based on the identification of 5,376 cross-links, we investigated protein-protein interactions and structures of lysosome- and endosome-related proteins. In particular, we present evidence for a tetrameric assembly of the lysosomal hydrolase PPT1 and heterodimeric/- multimeric structures of FLOT1/FLOT2 at lysosomes and early endosomes. For FLOT1-/FLOT2- positive early endosomes, we identified >300 proteins presenting putative cargo, and confirm the latrophilin family of adhesion G protein-coupled receptors as substrates for flotillin-dependent endocytosis.

Competing Interest Statement

The authors have declared no competing interest.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
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Posted January 12, 2022.
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Cross-linking of the Endolysosomal System Reveals Flotillin Structures and Putative Cargo
Jasjot Singh, Hadeer Elhabashy, Pathma Muthukottiappan, Markus Stepath, Martin Eisenacher, Oliver Kohlbacher, Volkmar Gieselmann, Dominic Winter
bioRxiv 2022.01.12.475930; doi: https://doi.org/10.1101/2022.01.12.475930
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Cross-linking of the Endolysosomal System Reveals Flotillin Structures and Putative Cargo
Jasjot Singh, Hadeer Elhabashy, Pathma Muthukottiappan, Markus Stepath, Martin Eisenacher, Oliver Kohlbacher, Volkmar Gieselmann, Dominic Winter
bioRxiv 2022.01.12.475930; doi: https://doi.org/10.1101/2022.01.12.475930

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