Novel interacting proteins identified by tandem affinity purification coupled to nano LC–MS/MS interact with ribosomal S6 protein kinase 4 (RSK4) and its variant protein (RSK4m)

Ribosomal S6 protein kinase 4 (RSK4) is an important novel tumor suppressor that inhibits breast cancer cell growth and induces senescence. However, RSK4m, which is a variant of RSK4 resulting from alternative splicing, may play distinct roles in some aspects. Knowledge about the mechanisms of RSK4 or RSK4m activity has been lacking. Analysis of the RSK4 and RSK4m interactome could provide insight into their specific functions and integrative mechanisms. Using tandem affinity purification, we obtained protein complexes that interacted with RSK4 or RSK4m. Mass spectrum analysis was performed to identify the obtained protein complexes, and bioinformatics analysis was performed. In this study, we isolated and identified 82 RSK4-associated proteins and 137 RSK4m-associated proteins using two STREP II and a single Flag tag-based tandem affinity purification (SF-TAP) coupled with nano LC–MS/MS in MDA-MB-231 cells. Gene Ontology and Ingenuity Pathway Analysis analyses provided functional annotations and protein-protein interaction networks of the protein interactome of RSK4 and RSK4m. Functional annotations of these proteins by bioinformatics analyses highlight the essential role of RSK4 and RSK4m in coordination with their interacting partners to mediate multiple biological processes, especially cell senescence. Moreover, after comparing the interactome of RSK4 and RSK4m, we found that RSK4m is involved in more molecular functions than RSK4.