Cross-linking of the endolysosomal system reveals potential flotillin structures and cargo

Jasjot Singh, Hadeer Elhabashy, Pathma Muthukottiappan, Markus Stepath, Martin Eisenacher, Oliver Kohlbacher, Volkmar Gieselmann and Dominic Winter ()
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Jasjot Singh: University of Bonn
Hadeer Elhabashy: Max-Planck-Institute for Developmental Biology
Pathma Muthukottiappan: University of Bonn
Markus Stepath: Ruhr-University Bochum
Martin Eisenacher: Ruhr-University Bochum
Oliver Kohlbacher: University of Tübingen
Volkmar Gieselmann: University of Bonn
Dominic Winter: University of Bonn

Nature Communications, 2022, vol. 13, issue 1, 1-18

Abstract: Abstract 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 analyze lysosomes and early endosomes. Based on the identification of 5376 cross-links, we investigate 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 a heterodimeric structure of FLOT1/FLOT2 at lysosomes and early endosomes. For FLOT1-/FLOT2-positive early endosomes, we identify >300 putative cargo proteins and confirm eleven substrates for flotillin-dependent endocytosis, including the latrophilin family of adhesion G protein-coupled receptors.

Date: 2022
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DOI: 10.1038/s41467-022-33951-0

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