The solute carrier superfamily interactome

Solute carrier (SLC) transporters form a protein superfamily that enables transmembrane transport of a wide range of substrates including nutrients, vitamins, ions and drugs. There are about 450 different SLCs, residing in cellular and a variety of subcellular membranes, and playing a vital role in cellular homeostasis and metabolic regulation. Loss-of-function of an unusually high proportion of SLC transporters is genetically associated with a plethora of human diseases, making them a rapidly emerging but challenging drug target class. Knowledge of the protein environment of transporters may elucidate the molecular basis for their functional integration with metabolic and cellular pathways and help conceive pharmacological interventions based on modulating proteostatic regulations, including functional restoration. We aimed at obtaining a global survey of the SLC protein interaction landscape by using a robust, standardized, one-step interaction proteomics protocol. We mapped the protein-protein interactions of 396 SLCs, covering thousands of novel relationships, to be assessed individually in the future using transporter-specific assays. Network and clustering analysis allowed identification of proteins likely to affect the proteostatic regulation of transporters. We employed a streamlined functional assessment process based on RNA interference (RNAi)-genetic perturbation of cells and measurement of protein stability and localization, including some transport assays, to positively validate the functional role of over 50 new interactions. As an example, we detail the role of a SLC16A6 phospho-degron in the recruitment of a SKP1-CUL1-F-box protein E3 ligase, and the contributions of PDZ-domain proteins LIN7C and MPP1 to the subcellular localization of SLC43A2. Overall, our work provides insights into the complex molecular network of membrane transporters while offering the largest experimental mass spectrometry-derived membrane protein data set to date as a resource for the scientific community.