IGF2BP1 phosphorylation in the disordered linkers regulates ribonucleoprotein condensate formation and RNA metabolism

• Published in: Nature communications 2024-10, Vol.15 (1), p.9054-26, Article 9054
• Main Authors: Hornegger, Harald, Anisimova, Aleksandra S., Muratovic, Adnan, Bourgeois, Benjamin, Spinetti, Elena, Niedermoser, Isabell, Covino, Roberto, Madl, Tobias, Karagöz, G. Elif
• Format: Article
• Language: English
• Subjects: 14/19; 49/91; 631/45/535/878/1263; 631/45/612/1230; 82/58; 82/6; 82/81; 82/83; Affinity; Assembly; Cell size; Condensates; Growth factors; HEK293 Cells; HeLa Cells; Humanities and Social Sciences; Humans; Localization; Metabolism; multidisciplinary; Mutants; Mutation; Phosphorylation; Protein Binding; Protein turnover; Proteins; Proteomics; Ribonucleoproteins - chemistry; Ribonucleoproteins - genetics; Ribonucleoproteins - metabolism; RNA - genetics; RNA - metabolism; RNA-binding protein; RNA-Binding Proteins - chemistry; RNA-Binding Proteins - genetics; RNA-Binding Proteins - metabolism; Science; Science (multidisciplinary); Transcriptomes
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-024-53400-4

The insulin-like growth factor 2 mRNA binding protein 1 (IGF2BP1) is a conserved RNA-binding protein that regulates RNA stability, localization and translation. IGF2BP1 is part of various ribonucleoprotein (RNP) condensates. However, the mechanism that regulates its assembly into condensates remains unknown. By using proteomics, we demonstrate that phosphorylation of IGF2BP1 at S181 in a disordered linker is regulated in a stress-dependent manner. Phosphomimetic mutations in two disordered linkers, S181E and Y396E, modulate RNP condensate formation by IGF2BP1 without impacting its binding affinity for RNA. Intriguingly, the S181E mutant, which lies in linker 1, impairs IGF2BP1 condensate formation in vitro and in cells, whereas a Y396E mutant in the second linker increases condensate size and dynamics. Structural approaches show that the first linker binds RNAs nonspecifically through its RGG/RG motif, an interaction weakened in the S181E mutant. Notably, linker 2 interacts with IGF2BP1’s folded domains and these interactions are partially impaired in the Y396E mutant. Importantly, the phosphomimetic mutants impact IGF2BP1’s interaction with RNAs and remodel the transcriptome in cells. Our data reveal how phosphorylation modulates low-affinity interaction networks in disordered linkers to regulate RNP condensate formation and RNA metabolism. How phosphorylation regulates the RNA-binding protein IGF2BP1 remained largely unclear. Here, the authors discovered that phosphorylation of IGF2BP1 in disordered linkers regulates its assembly into ribonucleoprotein granules and impacts metabolism of its target RNAs.