PDZD8 interacts with Protrudin and Rab7 at ER-late endosome membrane contact sites associated with mitochondria

Yael Elbaz-Alon,Michal Harel,Daniel E Quinnell,Nadav Segev,Tamar Geiger,Yuting Guo,Ori Avinoam,Dong Li,Jodi Nunnari

doi:10.1038/s41467-020-17451-7

Yael Elbaz-Alon, Michal Harel + Show 7 more

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https://doi.org/10.1038/s41467-020-17451-7

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Endosomes are compositionally dynamic organelles that regulate signaling, nutrient status and organelle quality by specifying whether material entering the cells will be shuttled back to the cell surface or degraded by the lysosome. Recently, membrane contact sites (MCSs) between the endoplasmic reticulum (ER) and endosomes have emerged as important players in endosomal protein sorting, dynamics and motility. Here, we show that PDZD8, a Synaptotagmin-like Mitochondrial lipid-binding Proteins (SMP) domain-containing ER transmembrane protein, utilizes distinct domains to interact with Rab7-GTP and the ER transmembrane protein Protrudin and together these components localize to an ER-late endosome MCS. At these ER-late endosome MCSs, mitochondria are also recruited to form a three-way contact. Thus, our data indicate that PDZD8 is a shared component of two distinct MCSs and suggest a role for SMP-mediated lipid transport in the regulation of endosome function.

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Endosomes are compositionally dynamic organelles that regulate signaling, nutrient status and organelle quality by specifying whether material entering the cells will be shuttled back to the cell surface or degraded by the lysosome
Mass spectrometry analysis of crosslinked endogenous PDZD8 immunopurifications revealed that the predominant interactor was Protrudin, an integral endoplasmic reticulum (ER) protein previously shown to reside at ER-late endosome MCSs22 (Fig. 1a, left panel; list provided in Supplementary Dataset 1)
Mass spectrometry analysis of reciprocal immunopurifications of endogenous Protrudin from crosslinked cell extracts using a validated antiProtrudin antibody revealed that its predominant interactor was PDZD8 (Fig. 1a, right panel; list provided in Supplementary Dataset 2)

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Endosomes are compositionally dynamic organelles that regulate signaling, nutrient status and organelle quality by specifying whether material entering the cells will be shuttled back to the cell surface or degraded by the lysosome. We show that PDZD8, a Synaptotagmin-like Mitochondrial lipid-binding Proteins (SMP) domain-containing ER transmembrane protein, utilizes distinct domains to interact with Rab7-GTP and the ER transmembrane protein Protrudin and together these components localize to an ER-late endosome MCS. At these ER-late endosome MCSs, mitochondria are recruited to form a three-way contact. Structure-function analysis indicates that distinct domains of PDZD8 mediate interactions with Protrudin and Rab[7] and that PDZD8 and Protrudin are independently recruited to ER-late endosome MCSs. PDZD8 was previously identified as a component of an ER-mitochondria MCS, the identity of its mitochondrial partner is not known[27]. Our observations are consistent with the idea that ER-late endosomal contact sites are dynamic plastic structures that regulate endosomal behavior

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