Clathrin-coated vesicles (CCVs) internalize membrane and protein cargo in metazoans and plants and facilitate endocytosis as well as post-Golgi trafficking. The formation of clathrin-coated vesicles occurs not only at the plasma membrane, but also at the TGN/EE, a distinction enabled by the recruitment of clathrin by specific adaptor complexes localizing to either the plasma membrane or the TGN/EE (Reynolds et al. Plant Physiol 2018, Dahhan and Bednarek, FEBS Letters. 2022). Collectively, the initiation, maturation, internalization, and trafficking of CCVs occur through the actions of a large host of accessory proteins whose identities and functions are still being unraveled. Consequently, resolving the identities of clathrin-associated proteins, as well as of CCV cargo proteins, will yield critical information about the organelles between which CCVs traffic and in what biological contexts.
To that end, the Bednarek Lab recently completed a decade-long proteomics study of a pool of enriched endocytic and post-Golgi derived CCVs to which identified the proteins associated with plant CCVs (Dahhan and Reynolds et al. Plant Cell 2022). These identifications were supported with dimethyl labeling and immunoblotting to quantitate the relative enrichments and depletions of proteins associated with these CCVs, thereby providing context to the researcher interested in whether their protein of interest might function in CCV-mediated transport or be a cargo of CCV-mediated transport.
Beyond the identification of a core CCV proteome of 778 proteins with associated CCV-enrichment or -depletion metrics, this study yielded surprising findings about the evolutionary divergences in proteins associated with CCVs. First, the conserved adaptin complex, AP-4 appears in plants to be clathrin-associated, supporting a role for CCV transport in facilitating AP-4 mediated post-Golgi trafficking, in contrast to the paradigm in other eukaryotes. Second, the low abundance and apparent depletion of the known clathrin-mediated endocytosis adaptor, TPLATE complex in the CCV proteome suggested that this adaptor was more peripherally associated with the CCV in comparison to other endocytic adaptors functioning in tandem, such as AP-2, which was well represented in the proteome and strongly enriched with the purified CCVs. A collaboration with the lab of Jiri Friml at IST-Austria revealed that the origin of the low representation of TPLATE in the CCV proteome was the external localization of TPLATE on the endocytic vesicle relative to the clathrin coat, in contrast to AP-2, which is on the interior of the clathrin coat (Johnson et al. PNAS. 2021).