Mapping of the human solute carrier transporter protein interaction landscape

Solute carrier (SLC) transporters form a superfamily of membrane proteins facilitating transmembrane transport of a wide range of substrates. SLCs play a vital role in cellular homeostasis and metabolic regulation, as they control nutrient, ion and drug transport. They consist of about 450 members which locate in cellular membranes including subcellular compartments. To achieve fine-tuned transport functions necessary for proper metabolic homeostasis, transporters act in concert with numerous other membrane, cytoskeletal and proteostatic proteins.

More than half lack a well described interactome. We applied an AP-MS protocol tailored to transmembrane proteins to map the protein interaction network for more than 400 solute carriers. We further devised a ML-based scoring approach integrating scores of commonly used scoring tools (e.g. SAINT, CompPASS) and multiple quantitative and uniqueness features. The generated interactome covers more than 18"000 novel high-confidence protein interactions, therefore providing a basis for understanding the molecular regulation of this protein family.

Clustering and functional enrichment analysis revealed interaction partners throughout the life span of the transporters. The extracted subnetworks allowed us to link interactors to proteostatic regulation pathways, including protein translation and posttranslational modification processes. In addition, we identified close to stoichiometric interactions, revealing known and novel stable assemblies of SLCs with chaperone-proteins.

We performed a large-scale validation approach focusing on protein stability and localization changes upon genetic perturbation of prey proteins by RNAi. For 135 bait-prey combinations either approach was tested, with 40% showing a functional effect on the target SLC.

Our dataset empowers the identification of core regulatory modules in which SLCs are involved and further contributes to the understanding of the biological roles of this understudied family of proteins.