Uncovering nutrient-regulated surface proteins using stable isotope labeling with amino acids in cell culture (SILAC) proteomics

The presence of a protein at the cell surface is regulated by the exocytic and endocytic membrane trafficking pathways. We have recently discovered that the nutrient, or amino acids, plays a substantial role in promoting the endocytic membrane trafficking. Here we ask if the nutrient can regulate the cell surface presentation of proteins, which has not been addressed in the literature according to our knowledge. To that end, HeLa cells are labeled with heavy and light isotopes. In the forward labeling experiment, heavy and light cells are treated with DMEM and HBSS for 2 hours respectively. Cells are surface-biotinylated and are subsequently mixed, lysed and subjected to affinity purification by Streptavidin beads. Reverse labeling experiment is identically performed except that heavy and light cells are treated with HBSS and DMEM respectively. Our proteomics data demonstrate that many cell surface exposed proteins, such as signaling receptors, ligands, extracellular matrix proteins, trans-Golgi network cargo adaptor proteins and Golgi enzymes, can be regulated by the nutrient. Our study implies that the nutrient might play essential roles in intracellular membrane trafficking and in shaping a cell’s interactions with its environment.