Abstract Microtubule-dependent endosomal transport is crucial for polar growth, ensuring the precise distribution of cellular cargos such as proteins and mRNAs. However, the molecular mechanism linking mRNAs to the endosomal surface remains poorly understood. Here, we present a structural analysis of the key RNA-binding protein Rrm4 from Ustilago maydis . Our findings reveal a new type of MademoiseLLE domain featuring a seven-helical bundle that provides a distinct binding interface. A comparative analysis with the canonical MLLE domain of the poly(A)-binding protein Pab1 disclosed unique characteristics of both domains. Deciphering the MLLE binding code enabled prediction and verification of previously unknown Rrm4 interactors containing short linear motifs. Importantly, we demonstrated that the human MLLE domains, such as those of PABPC1 and UBR5, employed a similar principle to distinguish among interaction partners. Thus, our study provides unprecedented mechanistic insights into how structural variations in the widely distributed MLLE domain facilitates mRNA attachment during endosomal transport. Significance Polar growing cells, such as fungal hyphae and neurons, utilize endosomes to transport mRNAs along their microtubules. But how do these mRNAs precisely attach to endosomes? Our study addresses this question by investing the key mRNA transporter, Rrm4, in a fungal model microorganism. We uncovered new features of a protein-protein interaction domain that recognizes specific short linear motifs in binding partners. While this domain resembles one found in the poly(A)-binding protein, it exhibits distinct motif recognition. Deciphering the underlying binding code unveiled new interaction partners for Rrm4. The recognition system is used to form a resilient network of RNA-binding proteins (RBPs) and their interaction partners during endosomal transport. This principle is applicable to humans, highlighting its fundamental importance.

Deciphering the RNA-binding protein network during endosomal mRNA transport