A Proteomics Approach to Membrane Trafficking

Membrane trafficking, including that of integral membrane proteins as well as peripherally associated proteins, appears to be a vital process common to all eukaryotes. An important element of membrane trafficking is to determine the protein composition of the various endomembrane compartments. A major issue with such a compositional analysis is the difficulty of having to distinguish between resident components involved in specific tasks and the proteins that are in transit through the endomembrane system. Examples of resident proteins include components of the SNARE complex used to target membrane vesicles to different locations in the cell. In the case of functionally important residents, one would expect such proteins to have a fairly precise subcellular localization. In the case of proteins "passing through" an endosomal compartment en route to a final destination, one would expect to find the proteins colocalizing with many membrane compartments. As is evident from several Update articles in this issue, ambiguity exists when employing cytological techniques to identify specific endomembrane compartments, while markers identified based on homology may behave differently in plant cells. Therefore, a proteomics approach based on proteins that would traffic through various parts of the endomembrane system, such as plasma membrane (PM) receptors, would be a welcome addition to membrane-trafficking studies. PM receptors are highly dependent on correct trafficking for their eventual localization, their biological function, and finally their degradation, while recent evidence suggests that endocytosis of PM receptors is an integral part of their biological function. In this review, first, a short update on endocytosis and endosomal trafficking in Arabidopsis (Arabidopsis thaliana) is provided. In this section, we emphasize trafficking of PM receptors as a proteomics tool by looking at how the PM receptors traffic in a time-dependent fashion in order to determine the relationship between different endosomal compartments. Second, we describe the recent progress in advanced proteomics techniques such as localization of organelle proteins by isotope tagging (LOPIT), by which proteins are assigned to different endosomal compartments