Dissecting the binding behavior of the multi-RRM endosomal mRNA transporter Rrm4 [RNA-seq]

RNA-binding proteins (RBPs) are central players in determining the life cycle of RNA molecules. These proteins are often modular in arrangement, featuring multiple RNA-binding domains, to enhance RNA recognition and functionality. How these multiple RNA-binding domains within individual RBPs work in concert to recognize mRNA targets is still poorly studied. In the model fungus Ustilago maydis, the multi-RRM domain protein Rrm4 plays a key role in mediating the long-distance mRNA transport on the cytoplasmic surface of early endosomes, thereby precisely regulating spatiotemporal gene expression. Rrm4 contains three RNA-recognition motifs (RRMs), organized in an ELAV-like pattern: a tandem RRM domain (RRM1,2) and a separate third RRM domain (RRM3). Utilizing Rrm4 variants with mutations in the RRM domains, we conducted a differential iCLIP analysis to dissect the RNA recognition code of individual RRM domains. Our study reveals that Rrm4 exhibits two binding mode: (i) a one-to-one interaction where the third RRM domain alone binds RNAs by recognizing the shot UAUG motif. (ii) an intricate composite binding mode where all three RRM domains cooperatively bind RNA. Improtantly, our finding demonstrates that it is not the simple one-to-one interaction but rather the complex cooperative binding mode, involving all three RRM domains, is critical for Rrm4 function in maintaining the unipolar growth of the fungal hyphae. Overall design: Differential gene expression analysis comparing hyphal cells either lacking rrm4 gene or carrying mutations in one or all RRM domains of Rrm4 with wildtype hyphal cells expression functional Rrm4 protein.