The solute carrier superfamily interactome

<p><span>Solute carrier (SLC) transporters form a protein superfamily that enables</span><span> transmembrane transport of a wide range of substrates including nutrients, vitamins, </span><span>ions</span><span> and drugs</span><span>. There are about 450 different SLCs, </span><span>residing</span><span> 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</span><span> class</span><span>. Knowledge of the protein environment of transporters </span><span>may elucidate </span><span>the molecular basis for their functional integration with</span> <span>metabolic and cellular pathways </span><span>and </span><span>help conceive pharmacological interventions based on modulating </span><span>proteostatic</span><span> regulations</span><span>,</span><span> including functional rest</span><span>o</span><span>ration. We aimed at obtaining a global survey of the SLC protein interaction landscape by using </span><span>a </span><span>robust</span><span>,</span><span> standardized</span><span>,</span><span> one-step </span><span>interaction proteomics</span><span> protocol. We mapped the protein-protein interactions of 396 SLCs, covering thousands of novel </span><span>relationships</span><span>, to be assessed individually in the future using transporter-specific assays. Network and clustering analysis allowed </span><span>identification of </span><span>proteins likely to affect the </span><span>proteostatic</span><span> 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 </span><span>validate</span><span> the functional role of over 50 </span><span>new </span><span>interactions. As an example, we</span> <span>d</span><span>etail</span><span> the role of a SLC16A6 phospho-degron in</span><span> the</span><span> 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 </span><span>experimental mass spectrometry-derived </span><span>membrane protein data</span> <span>set</span> <span>to date as a resource for the scientific community.</span></p>